diff --git a/src/main/ipc/repos.ts b/src/main/ipc/repos.ts
index d1b182108..0ccc0fcbd 100644
--- a/src/main/ipc/repos.ts
+++ b/src/main/ipc/repos.ts
@@ -87,7 +87,12 @@ import type { RepoMethod } from '../../shared/telemetry-events'
 import { detectRepoIconAndUpstream } from '../repo-icon-autodetect'
 import { enrichMissingRepoGitRemoteIdentities } from '../repo-git-remote-identity-enrichment'
 import { getProjectHostSetupForRepo } from '../../shared/project-host-setup-projection'
-import { normalizeExecutionHostId, parseExecutionHostId } from '../../shared/execution-host'
+import {
+  getRepoExecutionHostId,
+  normalizeExecutionHostId,
+  parseExecutionHostId,
+  type ExecutionHostId
+} from '../../shared/execution-host'
 import { joinRemotePath } from '../ssh/ssh-remote-platform'
 import {
   assertFolderWorkspacePathUsable,
@@ -2430,8 +2435,11 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
 
   ipcMain.handle(
     'repos:getBaseRefDefault',
-    async (_event, args: { repoId: string }): Promise<BaseRefDefaultResult> => {
-      const repo = store.getRepo(args.repoId)
+    async (
+      _event,
+      args: { repoId: string; hostId?: ExecutionHostId }
+    ): Promise<BaseRefDefaultResult> => {
+      const repo = getRepoForExecutionHost(store, args.repoId, args.hostId)
       if (!repo || isFolderRepo(repo)) {
         // Why: folder-mode repos have no git state to resolve a base ref from.
         // Return null + 0 so the renderer can decline to use a fabricated default
@@ -2507,14 +2515,20 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
 
   ipcMain.handle(
     'repos:searchBaseRefs',
-    async (_event, args: { repoId: string; query: string; limit?: number }) => {
+    async (
+      _event,
+      args: { repoId: string; query: string; limit?: number; hostId?: ExecutionHostId }
+    ) => {
       return (await searchBaseRefDetailsForRepo(store, args)).map((entry) => entry.refName)
     }
   )
 
   ipcMain.handle(
     'repos:searchBaseRefDetails',
-    async (_event, args: { repoId: string; query: string; limit?: number }) => {
+    async (
+      _event,
+      args: { repoId: string; query: string; limit?: number; hostId?: ExecutionHostId }
+    ) => {
       return searchBaseRefDetailsForRepo(store, args)
     }
   )
@@ -2522,9 +2536,9 @@ export function registerRepoHandlers(mainWindow: BrowserWindow, store: Store): v
 
 async function searchBaseRefDetailsForRepo(
   store: Store,
-  args: { repoId: string; query: string; limit?: number }
+  args: { repoId: string; query: string; limit?: number; hostId?: ExecutionHostId }
 ): Promise<BaseRefSearchResult[]> {
-  const repo = store.getRepo(args.repoId)
+  const repo = getRepoForExecutionHost(store, args.repoId, args.hostId)
   if (!repo || isFolderRepo(repo)) {
     return []
   }
@@ -2602,6 +2616,23 @@ async function searchBaseRefDetailsForRepo(
   return searchBaseRefDetails(repo.path, args.query, limit)
 }
 
+function getRepoForExecutionHost(
+  store: Store,
+  repoId: string,
+  hostId?: ExecutionHostId
+): Repo | null {
+  if (!hostId) {
+    return store.getRepo(repoId) ?? null
+  }
+  // Why: repo ids can collide across local and SSH hosts; base-ref reads must
+  // use the same host selected by the Settings pane as the subsequent write.
+  return (
+    store
+      .getRepos()
+      .find((repo) => repo.id === repoId && getRepoExecutionHostId(repo) === hostId) ?? null
+  )
+}
+
 function notifyReposChanged(mainWindow: BrowserWindow): void {
   if (!mainWindow.isDestroyed()) {
     mainWindow.webContents.send('repos:changed')
diff --git a/src/main/ipc/worktrees.test.ts b/src/main/ipc/worktrees.test.ts
index 9f4dea40f..c40e4ad06 100644
--- a/src/main/ipc/worktrees.test.ts
+++ b/src/main/ipc/worktrees.test.ts
@@ -8428,6 +8428,45 @@ describe('registerWorktreeHandlers', () => {
     expect(fsProvider.writeFile).not.toHaveBeenCalled()
   })
 
+  it('reads an issue-command override from the requested host when repo ids collide', async () => {
+    const localRepo = {
+      id: 'repo-shared',
+      path: '/local/repo',
+      displayName: 'local',
+      badgeColor: '#000',
+      addedAt: 0
+    }
+    const sshRepo = {
+      ...localRepo,
+      path: '/remote/repo',
+      displayName: 'ssh',
+      connectionId: 'conn-1'
+    }
+    const fsProvider = {
+      readFile: vi.fn(async (filePath: string) => {
+        if (filePath.endsWith('/.orca/issue-command')) {
+          return { content: 'remote command\n', isBinary: false }
+        }
+        throw Object.assign(new Error('missing'), { code: 'ENOENT' })
+      })
+    }
+    store.getRepos.mockReturnValue([localRepo, sshRepo])
+    store.getRepo.mockReturnValue(localRepo)
+    getSshFilesystemProviderMock.mockReturnValue(fsProvider)
+
+    await expect(
+      handlers['hooks:readIssueCommand'](null, {
+        repoId: 'repo-shared',
+        hostId: 'ssh:conn-1'
+      })
+    ).resolves.toMatchObject({
+      localContent: 'remote command',
+      effectiveContent: 'remote command',
+      source: 'local'
+    })
+    expect(fsProvider.readFile).toHaveBeenCalledWith('/remote/repo/.orca/issue-command')
+  })
+
   it('creates remote .gitignore only when it is missing while writing SSH issue commands', async () => {
     const repo = {
       id: 'repo-ssh',
diff --git a/src/main/ipc/worktrees.ts b/src/main/ipc/worktrees.ts
index 06397b341..a11a00127 100644
--- a/src/main/ipc/worktrees.ts
+++ b/src/main/ipc/worktrees.ts
@@ -2248,74 +2248,77 @@ export function registerWorktreeHandlers(
     )
   })
 
-  ipcMain.handle('hooks:readIssueCommand', async (_event, args: { repoId: string }) => {
-    const repo = store.getRepo(args.repoId)
-    if (!repo || isFolderRepo(repo)) {
-      return {
-        status: 'ok',
-        localContent: null,
-        sharedContent: null,
-        effectiveContent: null,
-        localFilePath: '',
-        source: 'none' as const
-      }
-    }
-    if (repo.connectionId) {
-      const issueCommandPath = joinWorktreeRelativePath(repo.path, '.orca/issue-command')
-      const fsProvider = getSshFilesystemProvider(repo.connectionId)
-      if (!fsProvider) {
+  ipcMain.handle(
+    'hooks:readIssueCommand',
+    async (_event, args: { repoId: string; hostId?: ExecutionHostId }) => {
+      const repo = getRepoForWorktreeRemoval(store, args.repoId, args.hostId)
+      if (!repo || isFolderRepo(repo)) {
         return {
-          status: 'error',
+          status: 'ok',
           localContent: null,
           sharedContent: null,
           effectiveContent: null,
-          localFilePath: issueCommandPath,
+          localFilePath: '',
           source: 'none' as const
         }
       }
+      if (repo.connectionId) {
+        const issueCommandPath = joinWorktreeRelativePath(repo.path, '.orca/issue-command')
+        const fsProvider = getSshFilesystemProvider(repo.connectionId)
+        if (!fsProvider) {
+          return {
+            status: 'error',
+            localContent: null,
+            sharedContent: null,
+            effectiveContent: null,
+            localFilePath: issueCommandPath,
+            source: 'none' as const
+          }
+        }
 
-      let status: 'ok' | 'error' = 'ok'
-      let localContent: string | null = null
-      let sharedContent: string | null = null
-      try {
-        const result = await fsProvider.readFile(issueCommandPath)
-        localContent = result.isBinary ? null : result.content.trim() || null
-      } catch (error) {
-        if (!isENOENT(error)) {
-          status = 'error'
+        let status: 'ok' | 'error' = 'ok'
+        let localContent: string | null = null
+        let sharedContent: string | null = null
+        try {
+          const result = await fsProvider.readFile(issueCommandPath)
+          localContent = result.isBinary ? null : result.content.trim() || null
+        } catch (error) {
+          if (!isENOENT(error)) {
+            status = 'error'
+          }
+        }
+        try {
+          const result = await fsProvider.readFile(joinWorktreeRelativePath(repo.path, 'orca.yaml'))
+          sharedContent = result.isBinary
+            ? null
+            : parseOrcaYaml(result.content)?.issueCommand?.trim() || null
+        } catch (error) {
+          if (!isENOENT(error)) {
+            status = 'error'
+          }
+        }
+        const effectiveContent = localContent ?? sharedContent
+        return {
+          status: localContent ? 'ok' : status,
+          localContent,
+          sharedContent,
+          effectiveContent,
+          localFilePath: issueCommandPath,
+          source: localContent
+            ? ('local' as const)
+            : sharedContent
+              ? ('shared' as const)
+              : ('none' as const)
         }
       }
-      try {
-        const result = await fsProvider.readFile(joinWorktreeRelativePath(repo.path, 'orca.yaml'))
-        sharedContent = result.isBinary
-          ? null
-          : parseOrcaYaml(result.content)?.issueCommand?.trim() || null
-      } catch (error) {
-        if (!isENOENT(error)) {
-          status = 'error'
-        }
-      }
-      const effectiveContent = localContent ?? sharedContent
-      return {
-        status: localContent ? 'ok' : status,
-        localContent,
-        sharedContent,
-        effectiveContent,
-        localFilePath: issueCommandPath,
-        source: localContent
-          ? ('local' as const)
-          : sharedContent
-            ? ('shared' as const)
-            : ('none' as const)
-      }
+      return readIssueCommand(repo.path)
     }
-    return readIssueCommand(repo.path)
-  })
+  )
 
   ipcMain.handle(
     'hooks:writeIssueCommand',
-    async (_event, args: { repoId: string; content: string }) => {
-      const repo = store.getRepo(args.repoId)
+    async (_event, args: { repoId: string; content: string; hostId?: ExecutionHostId }) => {
+      const repo = getRepoForWorktreeRemoval(store, args.repoId, args.hostId)
       if (!repo || isFolderRepo(repo)) {
         return
       }
diff --git a/src/preload/api-types.ts b/src/preload/api-types.ts
index 9151a2268..3aa7782f3 100644
--- a/src/preload/api-types.ts
+++ b/src/preload/api-types.ts
@@ -1020,12 +1020,21 @@ export type PreloadApi = {
     getDefaultCreateProjectParent: () => Promise<string>
     onCloneProgress: (callback: (data: { phase: string; percent: number }) => void) => () => void
     getGitUsername: (args: { repoId: string }) => Promise<string>
-    getBaseRefDefault: (args: { repoId: string }) => Promise<BaseRefDefaultResult>
-    searchBaseRefs: (args: { repoId: string; query: string; limit?: number }) => Promise<string[]>
+    getBaseRefDefault: (args: {
+      repoId: string
+      hostId?: ExecutionHostId
+    }) => Promise<BaseRefDefaultResult>
+    searchBaseRefs: (args: {
+      repoId: string
+      query: string
+      limit?: number
+      hostId?: ExecutionHostId
+    }) => Promise<string[]>
     searchBaseRefDetails: (args: {
       repoId: string
       query: string
       limit?: number
+      hostId?: ExecutionHostId
     }) => Promise<BaseRefSearchResult[]>
     onChanged: (callback: () => void) => () => void
   }
@@ -2242,7 +2251,7 @@ export type PreloadApi = {
       worktreePath: string
       command: string
     }) => Promise<WorktreeSetupLaunch>
-    readIssueCommand: (args: { repoId: string }) => Promise<{
+    readIssueCommand: (args: { repoId: string; hostId?: ExecutionHostId }) => Promise<{
       status?: 'ok' | 'error'
       localContent: string | null
       sharedContent: string | null
@@ -2250,7 +2259,11 @@ export type PreloadApi = {
       localFilePath: string
       source: 'local' | 'shared' | 'none'
     }>
-    writeIssueCommand: (args: { repoId: string; content: string }) => Promise<void>
+    writeIssueCommand: (args: {
+      repoId: string
+      content: string
+      hostId?: ExecutionHostId
+    }) => Promise<void>
   }
   ephemeralVm: {
     listRecipes: (args: { repoId: string }) => Promise<{
diff --git a/src/preload/index.ts b/src/preload/index.ts
index 1f0436caf..8342d8b10 100644
--- a/src/preload/index.ts
+++ b/src/preload/index.ts
@@ -598,16 +598,23 @@ const api = {
     getGitUsername: (args: { repoId: string }): Promise<string> =>
       ipcRenderer.invoke('repos:getGitUsername', args),
 
-    getBaseRefDefault: (args: { repoId: string }): Promise<BaseRefDefaultResult> =>
-      ipcRenderer.invoke('repos:getBaseRefDefault', args),
+    getBaseRefDefault: (args: {
+      repoId: string
+      hostId?: ExecutionHostId
+    }): Promise<BaseRefDefaultResult> => ipcRenderer.invoke('repos:getBaseRefDefault', args),
 
-    searchBaseRefs: (args: { repoId: string; query: string; limit?: number }): Promise<string[]> =>
-      ipcRenderer.invoke('repos:searchBaseRefs', args),
+    searchBaseRefs: (args: {
+      repoId: string
+      query: string
+      limit?: number
+      hostId?: ExecutionHostId
+    }): Promise<string[]> => ipcRenderer.invoke('repos:searchBaseRefs', args),
 
     searchBaseRefDetails: (args: {
       repoId: string
       query: string
       limit?: number
+      hostId?: ExecutionHostId
     }): Promise<BaseRefSearchResult[]> => ipcRenderer.invoke('repos:searchBaseRefDetails', args),
 
     onChanged: (callback: () => void): (() => void) => {
@@ -2639,6 +2646,7 @@ const api = {
 
     readIssueCommand: (args: {
       repoId: string
+      hostId?: ExecutionHostId
     }): Promise<{
       status?: 'ok' | 'error'
       localContent: string | null
@@ -2648,8 +2656,11 @@ const api = {
       source: 'local' | 'shared' | 'none'
     }> => ipcRenderer.invoke('hooks:readIssueCommand', args),
 
-    writeIssueCommand: (args: { repoId: string; content: string }): Promise<void> =>
-      ipcRenderer.invoke('hooks:writeIssueCommand', args)
+    writeIssueCommand: (args: {
+      repoId: string
+      content: string
+      hostId?: ExecutionHostId
+    }): Promise<void> => ipcRenderer.invoke('hooks:writeIssueCommand', args)
   },
 
   ephemeralVm: {
diff --git a/src/renderer/src/components/settings/BaseRefPicker.tsx b/src/renderer/src/components/settings/BaseRefPicker.tsx
index 23d6d347e..b0c0b6e72 100644
--- a/src/renderer/src/components/settings/BaseRefPicker.tsx
+++ b/src/renderer/src/components/settings/BaseRefPicker.tsx
@@ -10,9 +10,11 @@ import {
 } from '@/runtime/runtime-repo-client'
 import { isRuntimeRepoRefSearchQueryWithinLimit } from '@/runtime/runtime-repo-search-bounds'
 import { translate } from '@/i18n/i18n'
+import { parseExecutionHostId, type ExecutionHostId } from '../../../../shared/execution-host'
 
 type BaseRefPickerProps = {
   repoId: string
+  hostId?: ExecutionHostId
   currentBaseRef?: string
   onSelect: (ref: string) => void
   onUsePrimary?: () => void
@@ -20,13 +22,20 @@ type BaseRefPickerProps = {
 
 export function BaseRefPicker({
   repoId,
+  hostId,
   currentBaseRef,
   onSelect,
   onUsePrimary
 }: BaseRefPickerProps): React.JSX.Element {
-  const activeRuntimeEnvironmentId = useAppStore((state) =>
+  const focusedRuntimeEnvironmentId = useAppStore((state) =>
     getRuntimeEnvironmentIdForRepo(state, repoId)
   )
+  const selectedHost = parseExecutionHostId(hostId)
+  const activeRuntimeEnvironmentId = hostId
+    ? selectedHost?.kind === 'runtime'
+      ? selectedHost.environmentId
+      : null
+    : focusedRuntimeEnvironmentId
   // Why: null until the IPC resolves (or when the repo has no default base ref
   // available). We avoid seeding with 'origin/main' because that would display
   // a fabricated default in repos that don't actually have origin/main.
@@ -64,7 +73,11 @@ export function BaseRefPicker({
 
     const loadDefaultBaseRef = async (): Promise<void> => {
       try {
-        const result = await getRuntimeRepoBaseRefDefault({ activeRuntimeEnvironmentId }, repoId)
+        const result = await getRuntimeRepoBaseRefDefault(
+          { activeRuntimeEnvironmentId },
+          repoId,
+          hostId
+        )
         if (!stale) {
           setDefaultBaseRef(result.defaultBaseRef)
           setRemoteCount(result.remoteCount)
@@ -90,7 +103,7 @@ export function BaseRefPicker({
     return () => {
       stale = true
     }
-  }, [activeRuntimeEnvironmentId, repoId])
+  }, [activeRuntimeEnvironmentId, hostId, repoId])
 
   useEffect(() => {
     if (!isRuntimeRepoRefSearchQueryWithinLimit(baseRefQuery)) {
@@ -109,7 +122,13 @@ export function BaseRefPicker({
     setIsSearchingBaseRefs(true)
 
     const timer = window.setTimeout(() => {
-      void searchRuntimeRepoBaseRefs({ activeRuntimeEnvironmentId }, repoId, trimmedQuery, 20)
+      void searchRuntimeRepoBaseRefs(
+        { activeRuntimeEnvironmentId },
+        repoId,
+        trimmedQuery,
+        20,
+        hostId
+      )
         .then((results) => {
           if (!stale) {
             setBaseRefResults(results)
@@ -132,7 +151,7 @@ export function BaseRefPicker({
       stale = true
       window.clearTimeout(timer)
     }
-  }, [activeRuntimeEnvironmentId, baseRefQuery, repoId])
+  }, [activeRuntimeEnvironmentId, baseRefQuery, hostId, repoId])
 
   const effectiveBaseRef = currentBaseRef ?? defaultBaseRef
 
diff --git a/src/renderer/src/components/settings/RepositoryHooksSection.tsx b/src/renderer/src/components/settings/RepositoryHooksSection.tsx
index c10516dfd..1ee7cfe19 100644
--- a/src/renderer/src/components/settings/RepositoryHooksSection.tsx
+++ b/src/renderer/src/components/settings/RepositoryHooksSection.tsx
@@ -1,6 +1,6 @@
 /* eslint-disable max-lines -- Why: the script editor, advanced/Command Source disclosure, issue-command override, and YAML state surfaces share tightly coupled state and persistence; splitting them across files would scatter prop drilling. */
 /* oxlint-disable react-doctor/no-adjust-state-on-prop-change -- Why: repository hook saves and issue-command overrides synchronize debounced persistence state with external repo settings. */
-import { useCallback, useEffect, useRef, useState } from 'react'
+import { useCallback, useEffect, useMemo, useRef, useState } from 'react'
 import type {
   HookCommandSourcePolicy,
   OrcaHooks,
@@ -24,6 +24,7 @@ import { getRepositoryLocalCommandsSectionId } from './repository-settings-targe
 import { matchesSettingsSearch } from './settings-search'
 import { translate } from '@/i18n/i18n'
 import { getRepositoryHookScriptTextareaRows } from '@/lib/script-textarea-rows'
+import { getRepoExecutionHostId, parseExecutionHostId } from '../../../../shared/execution-host'
 
 type RepositoryHooksSectionProps = {
   repo: Repo
@@ -749,8 +750,15 @@ export function RepositoryHooksSection({
   // Why: this component uses the lightweight translate() helper; subscribe here
   // so render-time option/copy builders refresh when the UI language changes.
   useTranslation()
-  const settings = useAppStore((s) => s.settings)
   const settingsSearchQuery = useAppStore((s) => s.settingsSearchQuery)
+  const selectedHostId = getRepoExecutionHostId(repo)
+  const repoHostIdentity = `${selectedHostId}\0${repo.id}`
+  const hookRuntimeSettings = useMemo(() => {
+    const parsedHost = parseExecutionHostId(selectedHostId)
+    return {
+      activeRuntimeEnvironmentId: parsedHost?.kind === 'runtime' ? parsedHost.environmentId : null
+    }
+  }, [selectedHostId])
   const yamlState = yamlHooks
     ? 'loaded'
     : hasHooksFile
@@ -764,7 +772,7 @@ export function RepositoryHooksSection({
   )
   const hookSettingsDraftRef = useRef(hookSettingsDraft)
   hookSettingsDraftRef.current = hookSettingsDraft
-  const localCommandsRepoIdRef = useRef(repo.id)
+  const localCommandsRepoIdentityRef = useRef(repoHostIdentity)
   const localCommandsDraftDirtyRef = useRef(false)
   const localCommandsAutosaveTimerRef = useRef<number | null>(null)
   const persistRef = useRef(onUpdateHookSettings)
@@ -878,7 +886,7 @@ export function RepositoryHooksSection({
   // dirty draft through the previous repo's captured updater.
   useEffect(() => {
     const next = getHookSettingsDraft(repo.hookSettings)
-    const isSameRepo = localCommandsRepoIdRef.current === repo.id
+    const isSameRepo = localCommandsRepoIdentityRef.current === repoHostIdentity
 
     if (isSameRepo) {
       localCommandsPersistForRepoRef.current = onUpdateHookSettings
@@ -889,11 +897,17 @@ export function RepositoryHooksSection({
     }
 
     flushScriptDraft(localCommandsPersistForRepoRef.current)
-    localCommandsRepoIdRef.current = repo.id
+    localCommandsRepoIdentityRef.current = repoHostIdentity
     localCommandsPersistForRepoRef.current = onUpdateHookSettings
     hookSettingsDraftRef.current = next
     setHookSettingsDraft(next)
-  }, [flushScriptDraft, onUpdateHookSettings, repo.id, repo.hookSettings, syncHookSettingsDraft])
+  }, [
+    flushScriptDraft,
+    onUpdateHookSettings,
+    repo.hookSettings,
+    repoHostIdentity,
+    syncHookSettingsDraft
+  ])
 
   useEffect(() => {
     let cancelled = false
@@ -903,7 +917,9 @@ export function RepositoryHooksSection({
     setHasSharedIssueCommand(false)
     setIssueCommandSaveError(null)
 
-    void readRuntimeIssueCommand(settings, repoId)
+    // Why: the pane can show a host other than the globally focused runtime;
+    // route both runtime RPC and local/SSH IPC by the selected repo owner.
+    void readRuntimeIssueCommand(hookRuntimeSettings, repoId, selectedHostId)
       .then((result) => {
         if (cancelled) {
           return
@@ -925,18 +941,20 @@ export function RepositoryHooksSection({
       cancelled = true
       const draft = issueCommandDraftRef.current.trim()
       if (draft !== lastCommittedIssueCommandRef.current) {
-        void writeRuntimeIssueCommand(settings, repoId, draft).catch((err) => {
-          console.error('[RepositoryHooksSection] Failed to save issue command on unmount:', err)
-        })
+        void writeRuntimeIssueCommand(hookRuntimeSettings, repoId, draft, selectedHostId).catch(
+          (err) => {
+            console.error('[RepositoryHooksSection] Failed to save issue command on unmount:', err)
+          }
+        )
       }
     }
-  }, [repo.id, settings])
+  }, [hookRuntimeSettings, repo.id, repoHostIdentity, selectedHostId])
 
   const commitIssueCommand = useCallback(async (): Promise<void> => {
     const trimmed = issueCommandDraft.trim()
     setIssueCommandDraft(trimmed)
     try {
-      await writeRuntimeIssueCommand(settings, repo.id, trimmed)
+      await writeRuntimeIssueCommand(hookRuntimeSettings, repo.id, trimmed, selectedHostId)
       lastCommittedIssueCommandRef.current = trimmed
       setIssueCommandSaveError(null)
     } catch (err) {
@@ -945,7 +963,7 @@ export function RepositoryHooksSection({
       setIssueCommandSaveError(message)
       toast.error(message)
     }
-  }, [issueCommandDraft, repo.id, settings])
+  }, [hookRuntimeSettings, issueCommandDraft, repo.id, selectedHostId])
 
   const sharedSetupScript = yamlHooks?.scripts.setup
   const sharedArchiveScript = yamlHooks?.scripts.archive
diff --git a/src/renderer/src/components/settings/RepositoryHostSetupActions.tsx b/src/renderer/src/components/settings/RepositoryHostSetupActions.tsx
index 557de4db4..43be0d1f6 100644
--- a/src/renderer/src/components/settings/RepositoryHostSetupActions.tsx
+++ b/src/renderer/src/components/settings/RepositoryHostSetupActions.tsx
@@ -43,7 +43,7 @@ type RepositoryHostSetupActionsProps = {
     setupState: 'not-set-up'
     setupMethod: 'provisioned'
   }) => Promise<ProjectHostSetupCreateResult | null>
-  onOpenSetup: (repoId: string) => void
+  onSetupReady: (hostId: ExecutionHostId) => void
 }
 
 type SetupStep = 'choose' | 'existing' | 'clone' | 'planned'
@@ -55,7 +55,7 @@ export function RepositoryHostSetupActions({
   setupProjectExistingFolder,
   setupProjectClone,
   createProjectHostSetup,
-  onOpenSetup
+  onSetupReady
 }: RepositoryHostSetupActionsProps): React.JSX.Element | null {
   const [isOpen, setIsOpen] = useState(false)
   const [step, setStep] = useState<SetupStep>('choose')
@@ -102,7 +102,7 @@ export function RepositoryHostSetupActions({
       })
       if (result) {
         resetFlow()
-        onOpenSetup(result.repo.id)
+        onSetupReady(setupTargetHostId)
       }
     } finally {
       setIsSettingUp(false)
@@ -129,7 +129,7 @@ export function RepositoryHostSetupActions({
       })
       if (result) {
         resetFlow()
-        onOpenSetup(result.repo.id)
+        onSetupReady(setupTargetHostId)
       }
     } finally {
       setIsCloning(false)
diff --git a/src/renderer/src/components/settings/RepositoryHostSetupsSection.test.tsx b/src/renderer/src/components/settings/RepositoryHostSetupsSection.test.tsx
index 2ebc332f7..665ef0bcc 100644
--- a/src/renderer/src/components/settings/RepositoryHostSetupsSection.test.tsx
+++ b/src/renderer/src/components/settings/RepositoryHostSetupsSection.test.tsx
@@ -147,9 +147,10 @@ describe('RepositoryHostSetupsSection', () => {
     expect(container.textContent).toContain(LOCAL_HOST_LABEL)
   })
 
-  it('opens the selected host setup settings pane through the setup repo id', () => {
+  it('selects the host in place instead of navigating to a separate repo pane', () => {
     const openSettingsPage = vi.fn()
     const openSettingsTarget = vi.fn()
+    const setSettingsProjectHostSelection = vi.fn()
     const localRepo = makeRepo({
       id: 'local-repo',
       displayName: 'Orca',
@@ -181,7 +182,8 @@ describe('RepositoryHostSetupsSection', () => {
         })
       ],
       openSettingsPage,
-      openSettingsTarget
+      openSettingsTarget,
+      setSettingsProjectHostSelection
     })
 
     renderSection(localRepo)
@@ -196,8 +198,13 @@ describe('RepositoryHostSetupsSection', () => {
       openButton?.dispatchEvent(new MouseEvent('click', { bubbles: true }))
     })
 
-    expect(openSettingsPage).toHaveBeenCalledTimes(1)
-    expect(openSettingsTarget).toHaveBeenCalledWith({ pane: 'repo', repoId: 'remote-repo' })
+    // The single project pane switches host in place — no navigation.
+    expect(setSettingsProjectHostSelection).toHaveBeenCalledWith(
+      'github:stablyai/orca',
+      toSshExecutionHostId('openclaw 2')
+    )
+    expect(openSettingsPage).not.toHaveBeenCalled()
+    expect(openSettingsTarget).not.toHaveBeenCalled()
   })
 
   it('removes independent setup metadata instead of opening an empty repo target', async () => {
@@ -264,6 +271,7 @@ describe('RepositoryHostSetupsSection', () => {
   it('sets up the project on another known host from an existing folder path', async () => {
     const openSettingsPage = vi.fn()
     const openSettingsTarget = vi.fn()
+    const setSettingsProjectHostSelection = vi.fn()
     const setupProjectExistingFolder = vi.fn().mockResolvedValue({
       project: makeProject({ id: 'github:stablyai/orca' }),
       setup: makeSetup({
@@ -300,6 +308,7 @@ describe('RepositoryHostSetupsSection', () => {
       sshTargetLabels: new Map([['openclaw 2', 'openclaw 2']]),
       openSettingsPage,
       openSettingsTarget,
+      setSettingsProjectHostSelection,
       setupProjectExistingFolder
     })
 
@@ -327,13 +336,18 @@ describe('RepositoryHostSetupsSection', () => {
       kind: 'git',
       displayName: 'Orca'
     })
-    expect(openSettingsPage).toHaveBeenCalledTimes(1)
-    expect(openSettingsTarget).toHaveBeenCalledWith({ pane: 'repo', repoId: 'remote-repo' })
+    expect(setSettingsProjectHostSelection).toHaveBeenCalledWith(
+      'github:stablyai/orca',
+      'ssh:openclaw%202'
+    )
+    expect(openSettingsPage).not.toHaveBeenCalled()
+    expect(openSettingsTarget).not.toHaveBeenCalled()
   })
 
   it('clones the project onto another known host from settings', async () => {
     const openSettingsPage = vi.fn()
     const openSettingsTarget = vi.fn()
+    const setSettingsProjectHostSelection = vi.fn()
     const setupProjectClone = vi.fn().mockResolvedValue({
       project: makeProject({ id: 'github:stablyai/orca' }),
       setup: makeSetup({
@@ -370,6 +384,7 @@ describe('RepositoryHostSetupsSection', () => {
       sshTargetLabels: new Map([['openclaw 2', 'openclaw 2']]),
       openSettingsPage,
       openSettingsTarget,
+      setSettingsProjectHostSelection,
       setupProjectClone
     })
 
@@ -402,8 +417,12 @@ describe('RepositoryHostSetupsSection', () => {
       destination: '/home/alice',
       displayName: 'Orca'
     })
-    expect(openSettingsPage).toHaveBeenCalledTimes(1)
-    expect(openSettingsTarget).toHaveBeenCalledWith({ pane: 'repo', repoId: 'remote-repo' })
+    expect(setSettingsProjectHostSelection).toHaveBeenCalledWith(
+      'github:stablyai/orca',
+      'ssh:openclaw%202'
+    )
+    expect(openSettingsPage).not.toHaveBeenCalled()
+    expect(openSettingsTarget).not.toHaveBeenCalled()
   })
 
   it('creates pending setup metadata for a known host without requiring a path', async () => {
diff --git a/src/renderer/src/components/settings/RepositoryHostSetupsSection.tsx b/src/renderer/src/components/settings/RepositoryHostSetupsSection.tsx
index f149567f6..4506d04a0 100644
--- a/src/renderer/src/components/settings/RepositoryHostSetupsSection.tsx
+++ b/src/renderer/src/components/settings/RepositoryHostSetupsSection.tsx
@@ -1,5 +1,9 @@
 import { useMemo, useState } from 'react'
-import { getExecutionHostLabel } from '../../../../shared/execution-host'
+import {
+  getExecutionHostLabel,
+  getRepoExecutionHostId,
+  type ExecutionHostId
+} from '../../../../shared/execution-host'
 import { buildExecutionHostRegistry } from '../../../../shared/execution-host-registry'
 import { getHostDisplayLabelOverrides } from '../../../../shared/host-setting-overrides'
 import type { Repo } from '../../../../shared/types'
@@ -30,8 +34,9 @@ export function RepositoryHostSetupsSection({
   searchQuery,
   searchEntries
 }: RepositoryHostSetupsSectionProps): React.JSX.Element | null {
-  const openSettingsPage = useAppStore((state) => state.openSettingsPage)
-  const openSettingsTarget = useAppStore((state) => state.openSettingsTarget)
+  const setSettingsProjectHostSelection = useAppStore(
+    (state) => state.setSettingsProjectHostSelection
+  )
   const setupProjectExistingFolder = useAppStore((state) => state.setupProjectExistingFolder)
   const setupProjectClone = useAppStore((state) => state.setupProjectClone)
   const createProjectHostSetup = useAppStore((state) => state.createProjectHostSetup)
@@ -67,8 +72,9 @@ export function RepositoryHostSetupsSection({
   const projectHostSetupProjection = useAppStore((state) =>
     getProjectHostSetupProjectionFromState(state)
   )
+  const selectedHostId = getRepoExecutionHostId(repo)
   const selectedProjectHostSetup = projectHostSetupProjection.setups.find(
-    (setup) => setup.repoId === repo.id
+    (setup) => setup.repoId === repo.id && setup.hostId === selectedHostId
   )
   const projectHostSetups = selectedProjectHostSetup
     ? projectHostSetupProjection.setups.filter(
@@ -82,11 +88,14 @@ export function RepositoryHostSetupsSection({
   })
   const hostOptionById = new Map(hostOptions.map((option) => [option.id, option]))
   const [deletingSetupId, setDeletingSetupId] = useState<string | null>(null)
-  const openSetup = (repoId: string) => {
-    openSettingsPage()
-    openSettingsTarget({ pane: 'repo', repoId })
+  const projectId = selectedProjectHostSetup?.projectId
+  // Why: the single project pane switches host in place — set the ephemeral
+  // per-project selection instead of navigating to a separate repo section.
+  const selectHost = (hostId: ExecutionHostId) => {
+    if (projectId) {
+      setSettingsProjectHostSelection(projectId, hostId)
+    }
   }
-
   if (
     (projectHostSetups.length <= 1 && setupHostOptions.length === 0) ||
     (!forceVisible && !matchesSettingsSearch(searchQuery, searchEntries))
@@ -116,12 +125,12 @@ export function RepositoryHostSetupsSection({
                 {translate('auto.components.settings.RepositoryPane.viewingHost', 'Viewing host')}
               </span>
               <Select
-                value={repo.id}
-                onValueChange={(repoId) => {
-                  if (repoId === repo.id) {
+                value={selectedHostId}
+                onValueChange={(hostId) => {
+                  if (hostId === selectedHostId) {
                     return
                   }
-                  openSetup(repoId)
+                  selectHost(hostId as ExecutionHostId)
                 }}
               >
                 <SelectTrigger className="h-8 w-44 min-w-0 text-xs">
@@ -129,7 +138,7 @@ export function RepositoryHostSetupsSection({
                 </SelectTrigger>
                 <SelectContent>
                   {openableProjectHostSetups.map((setup) => (
-                    <SelectItem key={setup.id} value={setup.repoId}>
+                    <SelectItem key={setup.hostId} value={setup.hostId}>
                       <span className="block min-w-0 truncate">
                         {hostOptionById.get(setup.hostId)?.label ??
                           getExecutionHostLabel(setup.hostId)}
@@ -150,12 +159,12 @@ export function RepositoryHostSetupsSection({
       </div>
       <div className="divide-y divide-border rounded-md border border-border">
         {projectHostSetups.map((setup) => {
-          const isCurrentSetup = setup.repoId === repo.id
+          const isCurrentSetup = setup.hostId === selectedHostId
           const canOpenSetup = setup.repoId.trim().length > 0
           const canRemoveSetup = !canOpenSetup && deletingSetupId !== setup.id
           return (
             <div
-              key={setup.id}
+              key={setup.hostId}
               className={cn(
                 'flex w-full items-start gap-3 px-3 py-2.5 text-left transition-colors',
                 isCurrentSetup ? 'bg-muted/30' : ''
@@ -189,7 +198,7 @@ export function RepositoryHostSetupsSection({
                   variant="outline"
                   size="sm"
                   onClick={() => {
-                    openSetup(setup.repoId)
+                    selectHost(setup.hostId)
                   }}
                 >
                   {translate('auto.components.settings.RepositoryPane.openSetup', 'Open')}
@@ -221,7 +230,7 @@ export function RepositoryHostSetupsSection({
           setupProjectExistingFolder={setupProjectExistingFolder}
           setupProjectClone={setupProjectClone}
           createProjectHostSetup={createProjectHostSetup}
-          onOpenSetup={openSetup}
+          onSetupReady={selectHost}
         />
       ) : null}
     </SearchableSetting>
diff --git a/src/renderer/src/components/settings/RepositoryIconPicker.tsx b/src/renderer/src/components/settings/RepositoryIconPicker.tsx
index 9a79b13e1..51edc955f 100644
--- a/src/renderer/src/components/settings/RepositoryIconPicker.tsx
+++ b/src/renderer/src/components/settings/RepositoryIconPicker.tsx
@@ -8,9 +8,8 @@ import { normalizeRepoBadgeColor } from '../../../../shared/repo-badge-color'
 import { Button } from '../ui/button'
 import { Label } from '../ui/label'
 import { RepoIconGlyph, getRepoLucideIconOptions } from '../repo/repo-icon'
-import { useAppStore } from '@/store'
 import { getActiveRuntimeTarget } from '@/runtime/runtime-rpc-client'
-import { getRuntimeEnvironmentIdForRepo } from '@/lib/repo-runtime-owner'
+import { getRepoExecutionHostId, parseExecutionHostId } from '../../../../shared/execution-host'
 import { useMountedRef } from '@/hooks/useMountedRef'
 import { RepositoryIconColorSection } from './RepositoryIconColorSection'
 import { RepositoryIconTabs } from './RepositoryIconTabs'
@@ -33,9 +32,9 @@ export function RepositoryIconPicker({
   const mountedRef = useMountedRef()
   // Why: resolve this repo's upstream/avatar on the host that owns it, not the
   // focused runtime.
-  const activeRuntimeEnvironmentId = useAppStore((state) =>
-    getRuntimeEnvironmentIdForRepo(state, repo.id)
-  )
+  const selectedHost = parseExecutionHostId(getRepoExecutionHostId(repo))
+  const activeRuntimeEnvironmentId =
+    selectedHost?.kind === 'runtime' ? selectedHost.environmentId : null
   const selectedLucideName = repo.repoIcon?.type === 'lucide' ? repo.repoIcon.name : null
   const selectedEmoji = repo.repoIcon?.type === 'emoji' ? repo.repoIcon.emoji : ''
   const selectedBadgeColor = normalizeRepoBadgeColor(repo.badgeColor) ?? DEFAULT_REPO_BADGE_COLOR
diff --git a/src/renderer/src/components/settings/RepositoryPane.tsx b/src/renderer/src/components/settings/RepositoryPane.tsx
index e05f13fae..bb178d3c1 100644
--- a/src/renderer/src/components/settings/RepositoryPane.tsx
+++ b/src/renderer/src/components/settings/RepositoryPane.tsx
@@ -7,6 +7,7 @@ import type {
   RepoHookSettings
 } from '../../../../shared/types'
 import { getRepoKindLabel, isFolderRepo } from '../../../../shared/repo-kind'
+import { getRepoExecutionHostId, type ExecutionHostId } from '../../../../shared/execution-host'
 import { Button } from '../ui/button'
 import { Label } from '../ui/label'
 import { Separator } from '../ui/separator'
@@ -47,7 +48,11 @@ type RepositoryPaneProps = {
   hasHooksFile: boolean
   hooksInspectionReady: boolean
   mayNeedUpdate: boolean
-  updateRepo: (repoId: string, updates: RepositoryPaneRepoUpdate) => void
+  updateRepo: (
+    repoId: string,
+    updates: RepositoryPaneRepoUpdate,
+    options?: { hostId?: ExecutionHostId }
+  ) => void
   removeProject: (repoId: string) => void
   project?: Project | null
   isLocalWindowsProject?: boolean
@@ -76,6 +81,16 @@ export function RepositoryPane({
   updateProject
 }: RepositoryPaneProps): React.JSX.Element {
   const isFolder = isFolderRepo(repo)
+  // Why: this pane renders the switcher-selected host's repo row. Bind every
+  // edit to that host so identity/host-specific writes land on the selected
+  // host, not findRepoForHost's focused-host fallback (the same-id/self-pair
+  // case where local and a runtime share one repo id).
+  const selectedHostId = getRepoExecutionHostId(repo)
+  const updateSelectedRepo = useCallback(
+    (repoId: string, updates: RepositoryPaneRepoUpdate) =>
+      updateRepo(repoId, updates, { hostId: selectedHostId }),
+    [updateRepo, selectedHostId]
+  )
   const searchQuery = useAppStore((state) => state.settingsSearchQuery)
   const settings = useAppStore((state) => state.settings)
   const runtimeSessionSummary = useAppStore(
@@ -119,7 +134,7 @@ export function RepositoryPane({
   }
 
   const updateSelectedRepoHookSettings = (nextSettings: RepoHookSettings) => {
-    updateRepo(repo.id, {
+    updateSelectedRepo(repo.id, {
       hookSettings: nextSettings
     })
   }
@@ -229,8 +244,8 @@ export function RepositoryPane({
               'Remove Project'
             )}
             description={translate(
-              'auto.components.settings.RepositoryPane.170624bdfb',
-              'Remove this project from Orca.'
+              'auto.components.settings.RepositoryPane.removeProjectAllHosts',
+              'Remove this project from Orca on all configured hosts.'
             )}
             keywords={[repo.displayName, 'delete', 'project', 'repository']}
             className="absolute top-0 right-0 z-10 w-auto max-w-none"
@@ -273,7 +288,7 @@ export function RepositoryPane({
             id={`repo-display-name-${repo.id}`}
             repoId={repo.id}
             storeValue={repo.displayName}
-            onTextChange={(text) => updateRepo(repo.id, { displayName: text })}
+            onTextChange={(text) => updateSelectedRepo(repo.id, { displayName: text })}
             className="h-9 text-sm"
           />
         </SearchableSetting>
@@ -298,7 +313,7 @@ export function RepositoryPane({
           id={getRepositoryIconSectionId(repo.id)}
           forceVisible={forceFullPaneForRepoMatch}
         >
-          <RepositoryIconPicker repo={repo} updateRepo={updateRepo} />
+          <RepositoryIconPicker repo={repo} updateRepo={updateSelectedRepo} />
         </SearchableSetting>
 
         {!isFolder ? (
@@ -327,14 +342,14 @@ export function RepositoryPane({
 
             <RepositoryForkSyncSection
               repo={repo}
-              updateRepo={updateRepo}
+              updateRepo={updateSelectedRepo}
               forceVisible={forceFullPaneForRepoMatch}
             />
 
             <RepositoryWorktreeDefaultsSection
               repo={repo}
               settings={settings}
-              updateRepo={updateRepo}
+              updateRepo={updateSelectedRepo}
               forceVisible={forceFullPaneForRepoMatch}
             />
           </>
@@ -347,13 +362,13 @@ export function RepositoryPane({
       <RepositorySourceControlAiSection
         key="source-control-ai"
         repo={repo}
-        updateRepo={updateRepo}
+        updateRepo={updateSelectedRepo}
       />
     ) : null,
     !isFolder &&
     !repo.connectionId &&
     (forceFullPaneForRepoMatch || matchesSettingsSearch(searchQuery, symlinkEntries)) ? (
-      <WorktreeSymlinksSection key="symlinks" repo={repo} updateRepo={updateRepo} />
+      <WorktreeSymlinksSection key="symlinks" repo={repo} updateRepo={updateSelectedRepo} />
     ) : null,
     !isFolder &&
     (forceFullPaneForRepoMatch || matchesSettingsSearch(searchQuery, sparsePresetEntries)) ? (
diff --git a/src/renderer/src/components/settings/RepositoryWorktreeDefaultsSection.tsx b/src/renderer/src/components/settings/RepositoryWorktreeDefaultsSection.tsx
index db262bd06..e9bef3715 100644
--- a/src/renderer/src/components/settings/RepositoryWorktreeDefaultsSection.tsx
+++ b/src/renderer/src/components/settings/RepositoryWorktreeDefaultsSection.tsx
@@ -5,6 +5,7 @@ import { BaseRefPicker } from './BaseRefPicker'
 import { RepoSettingsDraftInput } from './RepositorySettingsDraftInput'
 import { SearchableSetting } from './SearchableSetting'
 import { translate } from '@/i18n/i18n'
+import { getRepoExecutionHostId } from '../../../../shared/execution-host'
 
 type RepositoryWorktreeDefaultsUpdate = Pick<Repo, 'worktreeBasePath' | 'worktreeBaseRef'>
 
@@ -41,6 +42,7 @@ export function RepositoryWorktreeDefaultsSection({
         </Label>
         <BaseRefPicker
           repoId={repo.id}
+          hostId={getRepoExecutionHostId(repo)}
           currentBaseRef={repo.worktreeBaseRef}
           onSelect={(ref) => updateRepo(repo.id, { worktreeBaseRef: ref })}
           onUsePrimary={() => updateRepo(repo.id, { worktreeBaseRef: undefined })}
diff --git a/src/renderer/src/components/settings/Settings.load-performance.test.ts b/src/renderer/src/components/settings/Settings.load-performance.test.ts
index 521e9aa7b..6edea688f 100644
--- a/src/renderer/src/components/settings/Settings.load-performance.test.ts
+++ b/src/renderer/src/components/settings/Settings.load-performance.test.ts
@@ -1,9 +1,5 @@
 import { describe, expect, it } from 'vitest'
-import {
-  deriveNeededRepoIds,
-  deriveNeededSectionIds,
-  getRuntimeTargetIdentity
-} from './settings-load-performance'
+import { deriveNeededSectionIds } from './settings-load-performance'
 
 describe('Settings load-performance helpers', () => {
   it('keeps only eager and active sections mounted for empty search on first paint', () => {
@@ -66,18 +62,4 @@ describe('Settings load-performance helpers', () => {
 
     expect(needed.has('repo-a')).toBe(true)
   })
-
-  it('scopes repo hook checks to needed repo sections only', () => {
-    const neededRepoIds = deriveNeededRepoIds(
-      [{ id: 'a' }, { id: 'b' }, { id: 'c' }],
-      new Set(['general', 'repo-b'])
-    )
-
-    expect(neededRepoIds).toEqual(['b'])
-  })
-
-  it('normalizes runtime target identity for cache invalidation keys', () => {
-    expect(getRuntimeTargetIdentity({ activeRuntimeEnvironmentId: null })).toBe('local')
-    expect(getRuntimeTargetIdentity({ activeRuntimeEnvironmentId: '  env-1  ' })).toBe('env-1')
-  })
 })
diff --git a/src/renderer/src/components/settings/Settings.tsx b/src/renderer/src/components/settings/Settings.tsx
index 2d5a94122..2e0d2baa0 100644
--- a/src/renderer/src/components/settings/Settings.tsx
+++ b/src/renderer/src/components/settings/Settings.tsx
@@ -10,7 +10,7 @@ import {
   type MutableRefObject
 } from 'react'
 import { toast } from 'sonner'
-import type { GlobalSettings, OrcaHooks } from '../../../../shared/types'
+import type { GlobalSettings, OrcaHooks, ProjectHostSetup, Repo } from '../../../../shared/types'
 import type { SpeechModelState } from '../../../../shared/speech-types'
 import type {
   SourceControlAiSettings,
@@ -29,7 +29,11 @@ import {
   mergeFontSuggestions
 } from './SettingsConstants'
 import { DEFAULT_APP_FONT_FAMILY, getDefaultVoiceSettings } from '../../../../shared/constants'
-import { getRepoExecutionHostId, LOCAL_EXECUTION_HOST_ID } from '../../../../shared/execution-host'
+import {
+  getRepoExecutionHostId,
+  LOCAL_EXECUTION_HOST_ID,
+  parseExecutionHostId
+} from '../../../../shared/execution-host'
 import { GeneralPane } from './GeneralPane'
 import { BrowserPane } from './BrowserPane'
 import { AppearancePane } from './AppearancePane'
@@ -96,14 +100,18 @@ import {
   useInstalledAgentSkill
 } from '@/hooks/useInstalledAgentSkills'
 import { useActiveProjectSkillRuntime } from '@/hooks/useActiveProjectSkillRuntime'
-import {
-  deriveNeededRepoIds,
-  deriveNeededSectionIds,
-  getInitialMountedSectionIds,
-  getRuntimeTargetIdentity
-} from './settings-load-performance'
+import { deriveNeededSectionIds, getInitialMountedSectionIds } from './settings-load-performance'
 import { translate } from '@/i18n/i18n'
 import { getProjectHostSetupProjectionFromState } from '../../store/selectors'
+import { getRepoHostIdentity } from '../../store/slices/repo-host-identity'
+import {
+  buildRepoIdToHostSelection,
+  buildRepoIdToRepresentative,
+  buildSettingsProjectList,
+  getSettingsProjectHostRepo,
+  removeSettingsProjectFromAllHosts,
+  resolveSettingsTargetRepoId
+} from './settings-project-list'
 
 const DevToolsPane = import.meta.env.DEV
   ? lazy(() => import('./DevToolsPane').then((module) => ({ default: module.DevToolsPane })))
@@ -157,9 +165,16 @@ const SETTINGS_NAV_GROUP_BY_ID = new Map<string, SettingsNavGroupDefinition>(
 const SHORTCUTS_ESCAPE_CONFIRM_TOAST_ID = 'shortcuts-escape-confirm'
 const SHORTCUTS_ESCAPE_CONFIRM_WINDOW_MS = 2200
 
-function getSettingsSectionId(pane: SettingsNavTarget, repoId: string | null): string {
+function getSettingsSectionId(
+  pane: SettingsNavTarget,
+  repoId: string | null,
+  repoIdToRepresentative: Map<string, string>
+): string {
   if (pane === 'repo' && repoId) {
-    return `repo-${repoId}`
+    // Why: a `{pane:'repo', repoId}` target can name any host's repo row, but
+    // Settings now renders one collapsed pane per project — resolve to that
+    // project's representative section so the deep link lands.
+    return `repo-${repoIdToRepresentative.get(repoId) ?? repoId}`
   }
   return pane
 }
@@ -283,12 +298,36 @@ function Settings(): React.JSX.Element {
   const removeProject = useAppStore((s) => s.removeProject)
   const settingsNavigationTarget = useAppStore((s) => s.settingsNavigationTarget)
   const clearSettingsTarget = useAppStore((s) => s.clearSettingsTarget)
+  const settingsProjectHostSelection = useAppStore((s) => s.settingsProjectHostSelection)
+  const setSettingsProjectHostSelection = useAppStore((s) => s.setSettingsProjectHostSelection)
   const settingsSearchInputQuery = useAppStore((s) => s.settingsSearchInputQuery)
   const settingsSearchQuery = useAppStore((s) => s.settingsSearchQuery)
   const setSettingsSearchQuery = useAppStore((s) => s.setSettingsSearchQuery)
   const modelStates = useAppStore((s) => s.modelStates)
   const refreshModelStates = useAppStore((s) => s.refreshModelStates)
 
+  // Why: collapse repo rows into one entry per project (derived from repos so it
+  // matches the nav metadata exactly) — the source of truth for the pane list.
+  const settingsProjectList = useMemo(() => buildSettingsProjectList(repos), [repos])
+  const repoIdToRepresentative = useMemo(
+    () => buildRepoIdToRepresentative(settingsProjectList),
+    [settingsProjectList]
+  )
+  // Why: lets a deep-link's repoId select the owning project's host so
+  // host-specific subsection anchors exist under the now-selected host.
+  const repoIdToHostSelection = useMemo(
+    () => buildRepoIdToHostSelection(settingsProjectList),
+    [settingsProjectList]
+  )
+  // Why: the pane-level "Remove Project" removes the whole project (every host
+  // setup), not just the selected host — the per-host remove lives inside
+  // "Available Hosts".
+  const removeProjectAllHosts = useCallback(
+    (setups: readonly ProjectHostSetup[]): Promise<void> =>
+      removeSettingsProjectFromAllHosts(setups, removeProject),
+    [removeProject]
+  )
+
   const [repoHooksMap, setRepoHooksMap] = useState<
     Record<string, { hasHooks: boolean; hooks: OrcaHooks | null; mayNeedUpdate: boolean }>
   >({})
@@ -348,7 +387,6 @@ function Settings(): React.JSX.Element {
   const pendingScrollTargetRef = useRef<string | null>(null)
   const pendingSubsectionScrollFrameRef = useRef<number | null>(null)
   const repoHooksRequestSeqRef = useRef(0)
-  const repoHooksRuntimeIdentityRef = useRef<string>('local')
   const shortcutsEscapeConfirmUntilRef = useRef(0)
   const sourceControlAiWriteQueueRef = useRef<Promise<void>>(Promise.resolve())
 
@@ -499,8 +537,6 @@ function Settings(): React.JSX.Element {
     }
   }, [refreshModelStates, showDesktopOnlySettings])
 
-  const runtimeTargetIdentity = getRuntimeTargetIdentity(settings)
-
   useEffect(() => {
     const hasVisibleOverlay = (): boolean =>
       Array.from(
@@ -615,8 +651,22 @@ function Settings(): React.JSX.Element {
 
     const paneSectionId = getSettingsSectionId(
       settingsNavigationTarget.pane as SettingsNavTarget,
-      settingsNavigationTarget.repoId
+      settingsNavigationTarget.repoId,
+      repoIdToRepresentative
     )
+    // Why: couple the deep link to the in-pane host switcher before scrolling —
+    // select the target repo's host so its host-specific subsection anchor
+    // (e.g. `repo-<remoteId>-source-control-ai`) renders and the scroll lands.
+    const targetRepoId = resolveSettingsTargetRepoId(
+      settingsNavigationTarget,
+      repoIdToHostSelection.keys()
+    )
+    if (targetRepoId) {
+      const hostSelection = repoIdToHostSelection.get(targetRepoId)
+      if (hostSelection) {
+        setSettingsProjectHostSelection(hostSelection.projectId, hostSelection.hostId)
+      }
+    }
     pendingNavSectionRef.current = paneSectionId
     pendingScrollTargetRef.current = settingsNavigationTarget.sectionId ?? paneSectionId
     // Why: Appearance nests status-bar controls under a collapsed accordion;
@@ -640,7 +690,14 @@ function Settings(): React.JSX.Element {
     // scroll effect runs even when the visible section set is otherwise stable.
     setPendingNavRequestTick((tick) => tick + 1)
     clearSettingsTarget()
-  }, [clearSettingsTarget, settings, settingsNavigationTarget])
+  }, [
+    clearSettingsTarget,
+    repoIdToHostSelection,
+    repoIdToRepresentative,
+    setSettingsProjectHostSelection,
+    settings,
+    settingsNavigationTarget
+  ])
 
   // Why: only recompute scrollback mode when the row value actually changes,
   // not on every unrelated settings mutation.
@@ -805,71 +862,80 @@ function Settings(): React.JSX.Element {
     setMountedSectionIds(neededSectionIds)
   }
 
-  const neededRepoIds = useMemo(
-    () => deriveNeededRepoIds(repos, neededSectionIds),
-    [neededSectionIds, repos]
-  )
+  // Why: each mounted project pane renders its SELECTED host's repo, so hooks
+  // must load for that repo id — not the representative id parsed from the
+  // section string (they differ when a non-default host is selected).
+  const neededRepos = useMemo(() => {
+    const reposByHostIdentity = new Map<string, Repo>()
+    for (const settingsProject of settingsProjectList) {
+      if (!neededSectionIds.has(`repo-${settingsProject.representativeRepoId}`)) {
+        continue
+      }
+      const repo = getSettingsProjectHostRepo(
+        settingsProject,
+        repos,
+        settingsProjectHostSelection[settingsProject.projectId]
+      )
+      if (repo) {
+        reposByHostIdentity.set(getRepoHostIdentity(repo), repo)
+      }
+    }
+    return [...reposByHostIdentity.values()]
+  }, [neededSectionIds, repos, settingsProjectHostSelection, settingsProjectList])
 
   useEffect(() => {
-    const repoIdSet = new Set(repos.map((repo) => repo.id))
+    const repoHostIdentitySet = new Set(repos.map(getRepoHostIdentity))
     setRepoHooksMap((previous) => {
       const next = Object.fromEntries(
-        Object.entries(previous).filter(([repoId]) => repoIdSet.has(repoId))
+        Object.entries(previous).filter(([identity]) => repoHostIdentitySet.has(identity))
       ) as Record<string, { hasHooks: boolean; hooks: OrcaHooks | null; mayNeedUpdate: boolean }>
       return Object.keys(next).length === Object.keys(previous).length ? previous : next
     })
   }, [repos])
 
   useEffect(() => {
-    if (repoHooksRuntimeIdentityRef.current !== runtimeTargetIdentity) {
-      repoHooksRuntimeIdentityRef.current = runtimeTargetIdentity
-      repoHooksRequestSeqRef.current += 1
-      setRepoHooksMap({})
-    }
-  }, [runtimeTargetIdentity])
-
-  useEffect(() => {
-    if (neededRepoIds.length === 0) {
+    if (neededRepos.length === 0) {
       return
     }
 
     let stale = false
     const requestSeq = ++repoHooksRequestSeqRef.current
-    const repoById = new Map(repos.map((repo) => [repo.id, repo] as const))
+    const liveRepoHostIdentities = new Set(repos.map(getRepoHostIdentity))
 
     void Promise.all(
-      neededRepoIds.map(async (repoId) => {
-        const repo = repoById.get(repoId)
-        if (!repo) {
-          return
-        }
+      neededRepos.map(async (repo) => {
+        const repoHostIdentity = getRepoHostIdentity(repo)
         if (isFolderRepo(repo)) {
           setRepoHooksMap((previous) => {
-            if (previous[repoId]) {
+            if (previous[repoHostIdentity]) {
               return previous
             }
             return {
               ...previous,
-              [repoId]: { hasHooks: false, hooks: null, mayNeedUpdate: false }
+              [repoHostIdentity]: { hasHooks: false, hooks: null, mayNeedUpdate: false }
             }
           })
           return
         }
         try {
+          const hostId = getRepoExecutionHostId(repo)
+          const parsedHost = parseExecutionHostId(hostId)
           const result = await checkRuntimeHooks(
-            runtimeTargetIdentity === 'local'
-              ? { activeRuntimeEnvironmentId: null }
-              : { activeRuntimeEnvironmentId: runtimeTargetIdentity },
-            repoId
+            {
+              activeRuntimeEnvironmentId:
+                parsedHost?.kind === 'runtime' ? parsedHost.environmentId : null
+            },
+            repo.id,
+            hostId
           )
           if (stale || requestSeq !== repoHooksRequestSeqRef.current) {
             return
           }
           setRepoHooksMap((previous) => {
-            if (!repos.some((entry) => entry.id === repoId)) {
+            if (!liveRepoHostIdentities.has(repoHostIdentity)) {
               return previous
             }
-            return { ...previous, [repoId]: result }
+            return { ...previous, [repoHostIdentity]: result }
           })
         } catch {
           // Keep last known value on transient failures.
@@ -877,15 +943,15 @@ function Settings(): React.JSX.Element {
             return
           }
           setRepoHooksMap((previous) => {
-            if (!repos.some((entry) => entry.id === repoId)) {
+            if (!liveRepoHostIdentities.has(repoHostIdentity)) {
               return previous
             }
-            if (previous[repoId]) {
+            if (previous[repoHostIdentity]) {
               return previous
             }
             return {
               ...previous,
-              [repoId]: { hasHooks: false, hooks: null, mayNeedUpdate: false }
+              [repoHostIdentity]: { hasHooks: false, hooks: null, mayNeedUpdate: false }
             }
           })
         }
@@ -895,7 +961,7 @@ function Settings(): React.JSX.Element {
     return () => {
       stale = true
     }
-  }, [neededRepoIds, repos, runtimeTargetIdentity])
+  }, [neededRepos, repos])
 
   useEffect(() => {
     const scrollTargetId = pendingScrollTargetRef.current
@@ -1646,32 +1712,47 @@ function Settings(): React.JSX.Element {
                   ) : null}
                 </SettingsSection>
 
-                {repos.map((repo) => {
-                  const repoSectionId = `repo-${repo.id}`
-                  const repoHooksState = repoHooksMap[repo.id]
-                  const project = projectByRepoId.get(repo.id) ?? null
+                {settingsProjectList.map((settingsProject) => {
+                  const repoSectionId = `repo-${settingsProject.representativeRepoId}`
+                  // Why: render the switcher-selected host's repo row (validated
+                  // against live setups) so identity edits and host-specific
+                  // settings follow the "Available Hosts" selection.
+                  const repo = getSettingsProjectHostRepo(
+                    settingsProject,
+                    repos,
+                    settingsProjectHostSelection[settingsProject.projectId]
+                  )
+                  if (!repo) {
+                    return null
+                  }
+                  const repoHostIdentity = getRepoHostIdentity(repo)
+                  const repoHooksState = repoHooksMap[repoHostIdentity]
+                  const project = projectByRepoId.get(repo.id) ?? settingsProject.project
 
                   return (
                     <SettingsSection
-                      key={repo.id}
+                      key={repoSectionId}
                       id={repoSectionId}
                       title={translate(
                         'auto.components.settings.Settings.3bf149e873',
                         'Project Settings > {{value0}}',
-                        { value0: repo.displayName }
+                        { value0: project.displayName }
                       )}
                       description={repo.path}
                       searchEntries={getSectionSearchEntries(repoSectionId)}
                     >
                       {isSectionMounted(repoSectionId) ? (
+                        // Why: same-id hosts otherwise reuse drafts and effects
+                        // from the previously selected host inside this pane.
                         <RepositoryPane
+                          key={repoHostIdentity}
                           repo={repo}
                           yamlHooks={repoHooksState?.hooks ?? null}
                           hasHooksFile={repoHooksState?.hasHooks ?? false}
                           hooksInspectionReady={Boolean(repoHooksState)}
                           mayNeedUpdate={repoHooksState?.mayNeedUpdate ?? false}
                           updateRepo={updateRepo}
-                          removeProject={removeProject}
+                          removeProject={() => void removeProjectAllHosts(settingsProject.setups)}
                           project={project}
                           isLocalWindowsProject={
                             getRepoExecutionHostId(repo) === LOCAL_EXECUTION_HOST_ID &&
diff --git a/src/renderer/src/components/settings/WorktreeSymlinksSection.tsx b/src/renderer/src/components/settings/WorktreeSymlinksSection.tsx
index bdc7ed12d..33a918a9c 100644
--- a/src/renderer/src/components/settings/WorktreeSymlinksSection.tsx
+++ b/src/renderer/src/components/settings/WorktreeSymlinksSection.tsx
@@ -11,8 +11,8 @@ import {
   getWorktreeSymlinkPathFilterState,
   type WorktreeSymlinkPathSuggestion
 } from './worktree-symlink-path-filter'
-import { useAppStore } from '@/store'
 import { translate } from '@/i18n/i18n'
+import { getRepoExecutionHostId, LOCAL_EXECUTION_HOST_ID } from '../../../../shared/execution-host'
 
 type WorktreeSymlinksSectionProps = {
   repo: Repo
@@ -32,10 +32,11 @@ export function WorktreeSymlinksSection({
 }: WorktreeSymlinksSectionProps): React.JSX.Element {
   const [open, setOpen] = useState(false)
   const [query, setQuery] = useState('')
-  const activeRuntimeEnvironmentId = useAppStore((s) => s.settings?.activeRuntimeEnvironmentId)
 
   const paths = repo.symlinkPaths ?? EMPTY_WORKTREE_SYMLINK_PATHS
-  const useLocalDirectorySuggestions = !activeRuntimeEnvironmentId?.trim()
+  // Why: the pane may show a non-focused runtime host; only inspect the local
+  // filesystem when the switcher-selected repo is actually local.
+  const useLocalDirectorySuggestions = getRepoExecutionHostId(repo) === LOCAL_EXECUTION_HOST_ID
   const directorySuggestionKey = `${repo.path}\n${repo.connectionId ?? ''}`
   const [directorySuggestions, setDirectorySuggestions] = useState<DirectorySuggestionState>(
     () => ({
diff --git a/src/renderer/src/components/settings/settings-load-performance.ts b/src/renderer/src/components/settings/settings-load-performance.ts
index d20ed23be..0bd4d5239 100644
--- a/src/renderer/src/components/settings/settings-load-performance.ts
+++ b/src/renderer/src/components/settings/settings-load-performance.ts
@@ -1,13 +1,5 @@
-import type { GlobalSettings } from '../../../../shared/types'
-
 const EAGER_SECTION_IDS = new Set(['general'])
 
-export function getRuntimeTargetIdentity(
-  settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined
-): string {
-  return settings?.activeRuntimeEnvironmentId?.trim() || 'local'
-}
-
 export function deriveNeededSectionIds(args: {
   navSectionIds: string[]
   mountedSectionIds: Set<string>
@@ -37,13 +29,6 @@ export function deriveNeededSectionIds(args: {
   return next
 }
 
-export function deriveNeededRepoIds(
-  repos: readonly { id: string }[],
-  neededSectionIds: Set<string>
-): string[] {
-  return repos.map((repo) => repo.id).filter((repoId) => neededSectionIds.has(`repo-${repoId}`))
-}
-
 export function getInitialMountedSectionIds(): Set<string> {
   return new Set(EAGER_SECTION_IDS)
 }
diff --git a/src/renderer/src/components/settings/settings-project-list.test.ts b/src/renderer/src/components/settings/settings-project-list.test.ts
new file mode 100644
index 000000000..2c72e84d7
--- /dev/null
+++ b/src/renderer/src/components/settings/settings-project-list.test.ts
@@ -0,0 +1,257 @@
+import { describe, expect, it, vi } from 'vitest'
+import type { ProjectHostSetup, Repo } from '../../../../shared/types'
+import {
+  buildRepoIdToHostSelection,
+  buildRepoIdToRepresentative,
+  buildSettingsProjectList,
+  getSettingsProjectHostRepo,
+  getSettingsProjectRepresentativeRepoId,
+  removeSettingsProjectFromAllHosts,
+  resolveEffectiveProjectHost,
+  resolveSettingsTargetRepoId
+} from './settings-project-list'
+
+function makeRepo(overrides: Partial<Repo> & Pick<Repo, 'id'>): Repo {
+  return {
+    path: `/repos/${overrides.id}`,
+    displayName: overrides.id,
+    badgeColor: '#000',
+    addedAt: 0,
+    ...overrides
+  } satisfies Repo
+}
+
+function makeSetup(
+  overrides: Partial<ProjectHostSetup> & Pick<ProjectHostSetup, 'hostId'>
+): ProjectHostSetup {
+  return {
+    id: `${overrides.hostId}:${overrides.repoId ?? 'r'}`,
+    projectId: 'p',
+    repoId: overrides.repoId ?? 'r',
+    path: '/repo',
+    displayName: 'r',
+    setupState: 'ready',
+    setupMethod: 'legacy-repo',
+    createdAt: 0,
+    updatedAt: 0,
+    ...overrides
+  } satisfies ProjectHostSetup
+}
+
+const gitRemote = {
+  canonicalKey: 'gitlab.com/acme/app',
+  remoteName: 'origin',
+  remoteUrl: 'git@gitlab.com:acme/app.git'
+}
+
+describe('buildSettingsProjectList', () => {
+  it('collapses a git same-remote pair on two hosts (different ids) into one project', () => {
+    const repos: Repo[] = [
+      makeRepo({ id: 'local-1', gitRemoteIdentity: gitRemote }),
+      makeRepo({
+        id: 'remote-9',
+        gitRemoteIdentity: gitRemote,
+        executionHostId: 'runtime:home-mac'
+      })
+    ]
+
+    const projects = buildSettingsProjectList(repos)
+
+    expect(projects).toHaveLength(1)
+    expect(projects[0].setups).toHaveLength(2)
+    // Representative is the local host's repo.
+    expect(projects[0].representativeRepoId).toBe('local-1')
+  })
+
+  it('collapses a folder with the same id on local + runtime into one project', () => {
+    const repos: Repo[] = [
+      makeRepo({ id: 'folder-x', kind: 'folder' }),
+      makeRepo({ id: 'folder-x', kind: 'folder', executionHostId: 'runtime:home-mac' })
+    ]
+
+    const projects = buildSettingsProjectList(repos)
+
+    expect(projects).toHaveLength(1)
+    expect(projects[0].setups).toHaveLength(2)
+    expect(projects[0].representativeRepoId).toBe('folder-x')
+  })
+
+  it('keeps the representative stable when an unrelated host is removed', () => {
+    const withRuntime: Repo[] = [
+      makeRepo({ id: 'local-1', gitRemoteIdentity: gitRemote }),
+      makeRepo({
+        id: 'remote-9',
+        gitRemoteIdentity: gitRemote,
+        executionHostId: 'runtime:home-mac'
+      })
+    ]
+    const localOnly: Repo[] = [makeRepo({ id: 'local-1', gitRemoteIdentity: gitRemote })]
+
+    expect(buildSettingsProjectList(withRuntime)[0].representativeRepoId).toBe(
+      buildSettingsProjectList(localOnly)[0].representativeRepoId
+    )
+  })
+})
+
+describe('getSettingsProjectRepresentativeRepoId', () => {
+  it('prefers the local host setup', () => {
+    const setups = [
+      makeSetup({ hostId: 'runtime:home-mac', repoId: 'aaa' }),
+      makeSetup({ hostId: 'local', repoId: 'zzz' })
+    ]
+    expect(getSettingsProjectRepresentativeRepoId(setups)).toBe('zzz')
+  })
+
+  it('falls back to the lowest repoId when there is no local setup', () => {
+    const setups = [
+      makeSetup({ hostId: 'runtime:home-mac', repoId: 'zzz' }),
+      makeSetup({ hostId: 'ssh:box', repoId: 'aaa' })
+    ]
+    expect(getSettingsProjectRepresentativeRepoId(setups)).toBe('aaa')
+  })
+})
+
+describe('resolveEffectiveProjectHost', () => {
+  const setups = [
+    makeSetup({ hostId: 'local', repoId: 'local-1' }),
+    makeSetup({ hostId: 'runtime:home-mac', repoId: 'remote-9' })
+  ]
+
+  it('keeps a valid stored selection', () => {
+    expect(resolveEffectiveProjectHost(setups, 'runtime:home-mac')).toBe('runtime:home-mac')
+  })
+
+  it('falls back to local when the stored host no longer exists', () => {
+    expect(resolveEffectiveProjectHost(setups, 'runtime:gone')).toBe('local')
+  })
+
+  it('falls back to the first ready setup when there is no local host', () => {
+    const remoteSetups = [
+      makeSetup({ hostId: 'ssh:box', repoId: 'a', setupState: 'not-set-up' }),
+      makeSetup({ hostId: 'runtime:home-mac', repoId: 'b', setupState: 'ready' })
+    ]
+    expect(resolveEffectiveProjectHost(remoteSetups, 'runtime:gone')).toBe('runtime:home-mac')
+  })
+
+  it('returns undefined when there are no setups', () => {
+    expect(resolveEffectiveProjectHost([], 'local')).toBeUndefined()
+  })
+})
+
+describe('deep-link resolution', () => {
+  const repos: Repo[] = [
+    makeRepo({ id: 'local-1', gitRemoteIdentity: gitRemote }),
+    makeRepo({ id: 'remote-9', gitRemoteIdentity: gitRemote, executionHostId: 'runtime:home-mac' })
+  ]
+  const projects = buildSettingsProjectList(repos)
+
+  it('maps every host repoId to the representative section (getSettingsSectionId resolver)', () => {
+    const map = buildRepoIdToRepresentative(projects)
+    expect(map.get('remote-9')).toBe('local-1')
+    expect(map.get('local-1')).toBe('local-1')
+  })
+
+  it('maps a repoId to its owning project + host for selection', () => {
+    const map = buildRepoIdToHostSelection(projects)
+    expect(map.get('remote-9')).toEqual({
+      projectId: projects[0].projectId,
+      hostId: 'runtime:home-mac'
+    })
+  })
+
+  it('parses a repoId from a host-specific subsection sectionId', () => {
+    const repoIds = [...buildRepoIdToHostSelection(projects).keys()]
+    expect(
+      resolveSettingsTargetRepoId(
+        { repoId: null, sectionId: 'repo-remote-9-source-control-ai' },
+        repoIds
+      )
+    ).toBe('remote-9')
+  })
+
+  it('prefers an explicit target repoId over the sectionId', () => {
+    expect(
+      resolveSettingsTargetRepoId({ repoId: 'local-1', sectionId: 'repo-remote-9-icon' }, [
+        'local-1',
+        'remote-9'
+      ])
+    ).toBe('local-1')
+  })
+
+  it('disambiguates repo ids where one is a prefix of another (longest match wins)', () => {
+    expect(
+      resolveSettingsTargetRepoId({ repoId: null, sectionId: 'repo-app-2-icon' }, ['app', 'app-2'])
+    ).toBe('app-2')
+  })
+
+  it('resolves the remote host repo row when a remote host is selected', () => {
+    const hostSelection = buildRepoIdToHostSelection(projects).get('remote-9')
+    expect(getSettingsProjectHostRepo(projects[0], repos, hostSelection?.hostId)?.id).toBe(
+      'remote-9'
+    )
+  })
+
+  it('defaults to the local host repo row when no host is selected', () => {
+    expect(getSettingsProjectHostRepo(projects[0], repos, undefined)?.id).toBe('local-1')
+  })
+
+  it('distinguishes same-id repo rows by execution host', () => {
+    const sameIdRepos = [
+      makeRepo({ id: 'same-repo', gitRemoteIdentity: gitRemote }),
+      makeRepo({
+        id: 'same-repo',
+        gitRemoteIdentity: gitRemote,
+        executionHostId: 'runtime:home-mac',
+        path: '/remote/repo'
+      })
+    ]
+    const sameIdProjects = buildSettingsProjectList(sameIdRepos)
+
+    expect(
+      getSettingsProjectHostRepo(sameIdProjects[0], sameIdRepos, 'runtime:home-mac')?.path
+    ).toBe('/remote/repo')
+  })
+})
+
+describe('removeSettingsProjectFromAllHosts', () => {
+  it('removes every host setup with its own hostId and skips setups without a repo row', async () => {
+    const removeProject = vi.fn().mockResolvedValue(undefined)
+    const setups = [
+      makeSetup({ hostId: 'local', repoId: 'local-1' }),
+      makeSetup({ hostId: 'ssh:box', repoId: '  ' }),
+      makeSetup({ hostId: 'runtime:home-mac', repoId: 'remote-9' })
+    ]
+
+    await removeSettingsProjectFromAllHosts(setups, removeProject)
+
+    expect(removeProject.mock.calls).toEqual([
+      ['local-1', { hostId: 'local' }],
+      ['remote-9', { hostId: 'runtime:home-mac' }]
+    ])
+  })
+
+  it('awaits each host removal before starting the next', async () => {
+    let resolveFirst: (() => void) | undefined
+    const removeProject = vi
+      .fn()
+      .mockImplementationOnce(
+        () =>
+          new Promise<void>((resolve) => {
+            resolveFirst = resolve
+          })
+      )
+      .mockResolvedValue(undefined)
+    const setups = [
+      makeSetup({ hostId: 'local', repoId: 'local-1' }),
+      makeSetup({ hostId: 'runtime:home-mac', repoId: 'remote-9' })
+    ]
+
+    const pending = removeSettingsProjectFromAllHosts(setups, removeProject)
+    await Promise.resolve()
+    expect(removeProject).toHaveBeenCalledTimes(1)
+
+    resolveFirst?.()
+    await pending
+    expect(removeProject).toHaveBeenCalledTimes(2)
+  })
+})
diff --git a/src/renderer/src/components/settings/settings-project-list.ts b/src/renderer/src/components/settings/settings-project-list.ts
new file mode 100644
index 000000000..b9d6770b5
--- /dev/null
+++ b/src/renderer/src/components/settings/settings-project-list.ts
@@ -0,0 +1,194 @@
+import type { Project, ProjectHostSetup, Repo } from '../../../../shared/types'
+import {
+  getRepoExecutionHostId,
+  LOCAL_EXECUTION_HOST_ID,
+  type ExecutionHostId
+} from '../../../../shared/execution-host'
+import { projectHostSetupProjectionFromRepos } from '../../../../shared/project-host-setup-projection'
+
+export type SettingsProject = {
+  projectId: string
+  project: Project
+  setups: ProjectHostSetup[]
+  representativeRepoId: string
+}
+
+/**
+ * Which repo row identifies a project's single Settings nav row + pane. Pure
+ * over the project's setups so nav and panes derive the same id. Prefers the
+ * `local` host (the user's own machine) and otherwise the lowest repoId, so the
+ * id is stable unless that exact repo row is removed.
+ */
+export function getSettingsProjectRepresentativeRepoId(
+  setups: readonly ProjectHostSetup[]
+): string {
+  const localSetup = setups.find(
+    (setup) => setup.hostId === LOCAL_EXECUTION_HOST_ID && setup.repoId.trim().length > 0
+  )
+  if (localSetup) {
+    return localSetup.repoId
+  }
+  let lowest = ''
+  for (const setup of setups) {
+    const repoId = setup.repoId.trim()
+    if (repoId.length > 0 && (lowest === '' || repoId < lowest)) {
+      lowest = repoId
+    }
+  }
+  return lowest
+}
+
+/**
+ * Collapses repo rows into one entry per project so Settings renders per
+ * project, matching the rest of the app. Derived from repos alone (not the
+ * persisted projects/setups) so the nav and pane lists agree exactly.
+ */
+export function buildSettingsProjectList(repos: readonly Repo[]): SettingsProject[] {
+  const projection = projectHostSetupProjectionFromRepos(repos)
+  const setupsByProjectId = new Map<string, ProjectHostSetup[]>()
+  for (const setup of projection.setups) {
+    const projectSetups = setupsByProjectId.get(setup.projectId)
+    if (projectSetups) {
+      projectSetups.push(setup)
+    } else {
+      setupsByProjectId.set(setup.projectId, [setup])
+    }
+  }
+  return projection.projects.map((project) => {
+    // Why: Settings metadata is rebuilt as repos refresh across hosts; index
+    // setups once so many projects do not turn each refresh into an O(n²) scan.
+    const setups = setupsByProjectId.get(project.id) ?? []
+    return {
+      projectId: project.id,
+      project,
+      setups,
+      representativeRepoId: getSettingsProjectRepresentativeRepoId(setups)
+    }
+  })
+}
+
+/**
+ * The host whose settings the project pane should show. Validates the stored
+ * selection against the live setups so a disconnected/removed host never leaves
+ * the pane rendering off a dangling hostId: falls back to local, then the first
+ * ready setup, then the first setup.
+ */
+export function resolveEffectiveProjectHost(
+  setups: readonly ProjectHostSetup[],
+  selectedHostId: ExecutionHostId | undefined
+): ExecutionHostId | undefined {
+  if (setups.length === 0) {
+    return undefined
+  }
+  if (selectedHostId && setups.some((setup) => setup.hostId === selectedHostId)) {
+    return selectedHostId
+  }
+  const localSetup = setups.find((setup) => setup.hostId === LOCAL_EXECUTION_HOST_ID)
+  if (localSetup) {
+    return localSetup.hostId
+  }
+  const readySetup = setups.find((setup) => setup.setupState === 'ready')
+  return (readySetup ?? setups[0]).hostId
+}
+
+/** Maps every host's repoId to its project's representative repoId, so a
+ *  `{pane:'repo', repoId}` deep link resolves to the collapsed pane. */
+export function buildRepoIdToRepresentative(
+  projects: readonly SettingsProject[]
+): Map<string, string> {
+  const map = new Map<string, string>()
+  for (const settingsProject of projects) {
+    for (const setup of settingsProject.setups) {
+      if (setup.repoId.trim().length > 0) {
+        map.set(setup.repoId, settingsProject.representativeRepoId)
+      }
+    }
+  }
+  return map
+}
+
+/** Maps each host's repoId to its owning project + host, so a deep link can
+ *  select that host in the pane's "Available Hosts" switcher. */
+export function buildRepoIdToHostSelection(
+  projects: readonly SettingsProject[]
+): Map<string, { projectId: string; hostId: ExecutionHostId }> {
+  const map = new Map<string, { projectId: string; hostId: ExecutionHostId }>()
+  for (const settingsProject of projects) {
+    for (const setup of settingsProject.setups) {
+      if (setup.repoId.trim().length > 0 && !map.has(setup.repoId)) {
+        map.set(setup.repoId, { projectId: settingsProject.projectId, hostId: setup.hostId })
+      }
+    }
+  }
+  return map
+}
+
+/**
+ * The repo row a Settings deep link points at, from either an explicit repoId
+ * or a `repo-<id>-<subsection>` sectionId. repo ids can contain hyphens, so the
+ * sectionId is matched against known ids with the longest match winning.
+ */
+export function resolveSettingsTargetRepoId(
+  target: { repoId: string | null; sectionId?: string },
+  repoIds: Iterable<string>
+): string | null {
+  if (target.repoId) {
+    return target.repoId
+  }
+  const sectionId = target.sectionId
+  if (!sectionId || !sectionId.startsWith('repo-')) {
+    return null
+  }
+  let best: string | null = null
+  for (const repoId of repoIds) {
+    if (sectionId === `repo-${repoId}` || sectionId.startsWith(`repo-${repoId}-`)) {
+      if (best === null || repoId.length > best.length) {
+        best = repoId
+      }
+    }
+  }
+  return best
+}
+
+/**
+ * Removes a project's setup on every host it exists on. Sequential so each
+ * host's teardown + projection recompute don't interleave; setups without a
+ * repo row (planned/not-set-up hosts) have nothing to remove.
+ */
+export async function removeSettingsProjectFromAllHosts(
+  setups: readonly ProjectHostSetup[],
+  removeProject: (repoId: string, options: { hostId: ExecutionHostId }) => Promise<void>
+): Promise<void> {
+  for (const setup of setups) {
+    if (setup.repoId.trim().length > 0) {
+      await removeProject(setup.repoId, { hostId: setup.hostId })
+    }
+  }
+}
+
+/**
+ * The repo row the project pane should render for the given host selection.
+ * Shared by the pane and the hooks-loading effect so they always agree on which
+ * host's repo (id + host) is mounted — critical in the same-id/self-pair case.
+ */
+export function getSettingsProjectHostRepo(
+  settingsProject: SettingsProject,
+  repos: readonly Repo[],
+  selectedHostId: ExecutionHostId | undefined
+): Repo | undefined {
+  const effectiveHostId = resolveEffectiveProjectHost(settingsProject.setups, selectedHostId)
+  if (!effectiveHostId) {
+    return undefined
+  }
+  const effectiveSetup =
+    settingsProject.setups.find((setup) => setup.hostId === effectiveHostId) ??
+    settingsProject.setups[0]
+  return (
+    repos.find(
+      (repo) =>
+        repo.id === effectiveSetup.repoId && getRepoExecutionHostId(repo) === effectiveHostId
+    ) ??
+    repos.find((repo) => repo.id === effectiveSetup.repoId) ??
+    repos.find((repo) => repo.id === settingsProject.representativeRepoId)
+  )
+}
diff --git a/src/renderer/src/hooks/useSettingsNavigationMetadata.test.ts b/src/renderer/src/hooks/useSettingsNavigationMetadata.test.ts
index 59c2cca3d..8d17ab144 100644
--- a/src/renderer/src/hooks/useSettingsNavigationMetadata.test.ts
+++ b/src/renderer/src/hooks/useSettingsNavigationMetadata.test.ts
@@ -181,6 +181,42 @@ describe('settings navigation metadata', () => {
     expect(ids({ isDev: true, isWebClient: true })).not.toContain('dev')
   })
 
+  it('renders one repo nav section per project even across execution hosts', () => {
+    const gitRemote = {
+      canonicalKey: 'gitlab.com/acme/app',
+      remoteName: 'origin',
+      remoteUrl: 'git@gitlab.com:acme/app.git'
+    }
+    const sections = buildSettingsNavigationMetadata({
+      isMac: false,
+      isWindows: false,
+      isWebClient: false,
+      repos: [
+        {
+          id: 'local-1',
+          path: '/a',
+          displayName: 'App',
+          badgeColor: '#000',
+          addedAt: 0,
+          gitRemoteIdentity: gitRemote
+        },
+        {
+          id: 'remote-9',
+          path: '/b',
+          displayName: 'App',
+          badgeColor: '#000',
+          addedAt: 0,
+          gitRemoteIdentity: gitRemote,
+          executionHostId: 'runtime:home-mac'
+        }
+      ]
+    })
+
+    const repoSections = sections.filter((section) => section.id.startsWith('repo-'))
+    expect(repoSections).toHaveLength(1)
+    expect(repoSections[0].id).toBe('repo-local-1')
+  })
+
   it('keeps macOS permissions mac-only', () => {
     expect(ids({ isMac: false })).not.toContain('developer-permissions')
     expect(ids({ isMac: true })).toContain('developer-permissions')
diff --git a/src/renderer/src/hooks/useSettingsNavigationMetadata.ts b/src/renderer/src/hooks/useSettingsNavigationMetadata.ts
index 03ba64e44..e39c75db2 100644
--- a/src/renderer/src/hooks/useSettingsNavigationMetadata.ts
+++ b/src/renderer/src/hooks/useSettingsNavigationMetadata.ts
@@ -71,6 +71,7 @@ import { getShortcutsPaneSearchEntries } from '@/components/settings/shortcuts-s
 import { getStatsPaneSearchEntries } from '@/components/stats/stats-search'
 import { getExperimentalPaneSearchEntries } from '@/components/settings/experimental-search'
 import { getRepositoryPaneSearchEntries } from '@/components/settings/repository-search'
+import { buildSettingsProjectList } from '@/components/settings/settings-project-list'
 import { isWebClientLocation } from '@/lib/web-client-location'
 import {
   getWindowsTerminalCapabilityOwnerKey,
@@ -130,6 +131,12 @@ export function buildSettingsNavigationMetadata({
   const runtimeEnvironmentsSearchEntry = isWebClient
     ? getWebRuntimeEnvironmentsSearchEntry()
     : getRuntimeEnvironmentsSearchEntry()
+  const reposById = new Map<string, Repo>()
+  for (const repo of repos) {
+    if (!reposById.has(repo.id)) {
+      reposById.set(repo.id, repo)
+    }
+  }
 
   return [
     // Why: this array's order must mirror SETTINGS_NAV_GROUPS so the Settings
@@ -537,16 +544,30 @@ export function buildSettingsNavigationMetadata({
       searchEntries: getExperimentalPaneSearchEntries(),
       group: 'experimental'
     },
-    ...repos.map((repo) => ({
-      id: `repo-${repo.id}`,
-      title: repo.displayName,
-      description: `${getRepoKindLabel(repo)} • ${repo.path}`,
-      icon: SlidersHorizontal,
-      searchEntries: getRepositoryPaneSearchEntries(repo, {
-        windowsRuntimeSupported: isWindowsTerminalHost
-      }),
-      group: 'repositories'
-    }))
+    // Why: one nav row per project, not per repo row — a project set up on
+    // multiple hosts (local + a Remote Orca Server, or two clones) collapses to
+    // a single entry. Derived from repos alone so this list matches the panes.
+    ...buildSettingsProjectList(repos).map(({ project, representativeRepoId, setups }) => {
+      const representativeRepo = reposById.get(representativeRepoId) ?? repos[0]
+      const hostSummary =
+        setups.length > 1
+          ? translate(
+              'auto.hooks.useSettingsNavigationMetadata.projectHostsSummary',
+              '{{value0}} hosts',
+              { value0: setups.length }
+            )
+          : (setups[0]?.path ?? representativeRepo.path)
+      return {
+        id: `repo-${representativeRepoId}`,
+        title: project.displayName,
+        description: `${getRepoKindLabel(project)} • ${hostSummary}`,
+        icon: SlidersHorizontal,
+        searchEntries: getRepositoryPaneSearchEntries(representativeRepo, {
+          windowsRuntimeSupported: isWindowsTerminalHost
+        }),
+        group: 'repositories'
+      }
+    })
   ]
 }
 
diff --git a/src/renderer/src/i18n/locales/en.json b/src/renderer/src/i18n/locales/en.json
index 2e2ec2c60..d3f221f77 100644
--- a/src/renderer/src/i18n/locales/en.json
+++ b/src/renderer/src/i18n/locales/en.json
@@ -699,7 +699,8 @@
         "devSearchKeywordToast": "toast",
         "devSearchKeywordSonner": "sonner",
         "devSearchKeywordError": "error",
-        "devSearchKeywordNotification": "notification"
+        "devSearchKeywordNotification": "notification",
+        "projectHostsSummary": "{{value0}} hosts"
       },
       "useAppMenuPaste": {
         "pasteTooLarge": "Paste is too large."
@@ -6127,7 +6128,7 @@
           "26fef02bf3": "Project Icon",
           "c7ef4415de": "Display Name",
           "b0a0c14a1c": "Project-specific display details for the sidebar and tabs.",
-          "170624bdfb": "Remove this project from Orca.",
+          "removeProjectAllHosts": "Remove this project from Orca on all configured hosts.",
           "0909e5d650": "Remove Project",
           "ee5a290616": "Opened as folder. Git features are unavailable for this workspace.",
           "323debba71": "Type:",
diff --git a/src/renderer/src/i18n/locales/es.json b/src/renderer/src/i18n/locales/es.json
index 4790364ca..903467f92 100644
--- a/src/renderer/src/i18n/locales/es.json
+++ b/src/renderer/src/i18n/locales/es.json
@@ -699,7 +699,8 @@
         "devSearchKeywordToast": "toast",
         "devSearchKeywordSonner": "sonner",
         "devSearchKeywordError": "error",
-        "devSearchKeywordNotification": "notification"
+        "devSearchKeywordNotification": "notification",
+        "projectHostsSummary": "{{value0}} hosts"
       },
       "useAppMenuPaste": {
         "pasteTooLarge": "El contenido pegado es demasiado grande."
@@ -6090,7 +6091,7 @@
           "26fef02bf3": "Icono de proyecto",
           "c7ef4415de": "Nombre para mostrar",
           "b0a0c14a1c": "Detalles de visualización específicos del proyecto para la barra lateral y las pestañas.",
-          "170624bdfb": "Eliminar este proyecto de Orca.",
+          "removeProjectAllHosts": "Eliminar este proyecto de Orca en todos los hosts configurados.",
           "0909e5d650": "Eliminar proyecto",
           "ee5a290616": "Abierto como carpeta. Las funciones de Git no están disponibles para este espacio de trabajo.",
           "323debba71": "Tipo:",
diff --git a/src/renderer/src/i18n/locales/ja.json b/src/renderer/src/i18n/locales/ja.json
index c1845e376..123baa012 100644
--- a/src/renderer/src/i18n/locales/ja.json
+++ b/src/renderer/src/i18n/locales/ja.json
@@ -699,7 +699,8 @@
         "devSearchKeywordToast": "toast",
         "devSearchKeywordSonner": "sonner",
         "devSearchKeywordError": "error",
-        "devSearchKeywordNotification": "notification"
+        "devSearchKeywordNotification": "notification",
+        "projectHostsSummary": "{{value0}} 台のホスト"
       },
       "useAppMenuPaste": {
         "pasteTooLarge": "貼り付け内容が大きすぎます。"
@@ -6112,7 +6113,7 @@
           "26fef02bf3": "プロジェクトアイコン",
           "c7ef4415de": "表示名",
           "b0a0c14a1c": "サイドバーとタブのプロジェクト固有の表示詳細。",
-          "170624bdfb": "このプロジェクトを Orca から削除します。",
+          "removeProjectAllHosts": "このプロジェクトを、設定済みのすべてのホストの Orca から削除します。",
           "0909e5d650": "プロジェクトの削除",
           "ee5a290616": "フォルダーとして開きます。このワークスペースでは Git 機能を使用できません。",
           "323debba71": "タイプ：",
diff --git a/src/renderer/src/i18n/locales/ko.json b/src/renderer/src/i18n/locales/ko.json
index 48954ef52..e173a6e17 100644
--- a/src/renderer/src/i18n/locales/ko.json
+++ b/src/renderer/src/i18n/locales/ko.json
@@ -699,7 +699,8 @@
         "devSearchKeywordToast": "toast",
         "devSearchKeywordSonner": "sonner",
         "devSearchKeywordError": "error",
-        "devSearchKeywordNotification": "notification"
+        "devSearchKeywordNotification": "notification",
+        "projectHostsSummary": "호스트 {{value0}}개"
       },
       "useAppMenuPaste": {
         "pasteTooLarge": "붙여넣기 내용이 너무 큽니다."
@@ -6075,7 +6076,7 @@
           "26fef02bf3": "프로젝트 아이콘",
           "c7ef4415de": "표시 이름",
           "b0a0c14a1c": "사이드바 및 탭에 대한 프로젝트별 표시 세부 정보입니다.",
-          "170624bdfb": "Orca에서 이 프로젝트를 제거하세요.",
+          "removeProjectAllHosts": "구성된 모든 호스트의 Orca에서 이 프로젝트를 제거합니다.",
           "0909e5d650": "프로젝트 제거",
           "ee5a290616": "폴더로 열렸습니다. 이 워크스페이스에서는 Git 기능을 사용할 수 없습니다.",
           "323debba71": "유형:",
diff --git a/src/renderer/src/i18n/locales/zh.json b/src/renderer/src/i18n/locales/zh.json
index 7344a7f7a..a82d1d5fc 100644
--- a/src/renderer/src/i18n/locales/zh.json
+++ b/src/renderer/src/i18n/locales/zh.json
@@ -699,7 +699,8 @@
         "devSearchKeywordToast": "toast",
         "devSearchKeywordSonner": "sonner",
         "devSearchKeywordError": "error",
-        "devSearchKeywordNotification": "notification"
+        "devSearchKeywordNotification": "notification",
+        "projectHostsSummary": "{{value0}} 个主机"
       },
       "useAppMenuPaste": {
         "pasteTooLarge": "粘贴内容过大。"
@@ -6075,7 +6076,7 @@
           "26fef02bf3": "项目图标",
           "c7ef4415de": "显示名称",
           "b0a0c14a1c": "侧边栏和选项卡的项目特定显示详细信息。",
-          "170624bdfb": "从 Orca 中删除该项目。",
+          "removeProjectAllHosts": "从所有已配置主机的 Orca 中删除该项目。",
           "0909e5d650": "删除项目",
           "ee5a290616": "作为文件夹打开。 Git 功能对此工作区不可用。",
           "323debba71": "类型：",
diff --git a/src/renderer/src/lib/ensure-hooks-confirmed.test.ts b/src/renderer/src/lib/ensure-hooks-confirmed.test.ts
index da3d2028a..1bb0053da 100644
--- a/src/renderer/src/lib/ensure-hooks-confirmed.test.ts
+++ b/src/renderer/src/lib/ensure-hooks-confirmed.test.ts
@@ -368,6 +368,26 @@ describe('ensureHooksConfirmed', () => {
     expect(pending).toHaveLength(0)
   })
 
+  it('forwards the explicit host to issueCommand inspection when repo ids collide', async () => {
+    const { state } = createTestState({
+      repos: [
+        { id: 'repo-1', displayName: 'Local Row' },
+        { id: 'repo-1', displayName: 'SSH Row', connectionId: 'server' }
+      ]
+    } as unknown as Partial<AppState>)
+    readIssueCommandMock.mockResolvedValue({
+      source: 'local',
+      sharedContent: null,
+      localContent: 'user content',
+      effectiveContent: 'user content',
+      localFilePath: ''
+    })
+
+    await ensureHooksConfirmed(state, 'repo-1', 'issueCommand', 'ssh:server')
+
+    expect(readIssueCommandMock).toHaveBeenCalledWith({ repoId: 'repo-1', hostId: 'ssh:server' })
+  })
+
   it('fails closed when issueCommand inspection reports an error status', async () => {
     const { state, pending } = createTestState()
     readIssueCommandMock.mockResolvedValue({
diff --git a/src/renderer/src/lib/ensure-hooks-confirmed.ts b/src/renderer/src/lib/ensure-hooks-confirmed.ts
index 1ad0b7a7a..acb99840f 100644
--- a/src/renderer/src/lib/ensure-hooks-confirmed.ts
+++ b/src/renderer/src/lib/ensure-hooks-confirmed.ts
@@ -101,9 +101,12 @@ export async function ensureHooksConfirmed(
     try {
       if (scriptKind === 'issueCommand') {
         // Local overrides are user-owned; only shared orca.yaml commands need repo trust.
+        // Why: hostId disambiguates duplicate repo ids on the local IPC path,
+        // matching the checkRuntimeHooks call below.
         const result = await readRuntimeIssueCommand(
           settingsForHookRepoOwner(state, repoId, hostId),
-          repoId
+          repoId,
+          hostId
         )
         if (result.source === 'local') {
           return 'run'
diff --git a/src/renderer/src/runtime/runtime-hooks-client.test.ts b/src/renderer/src/runtime/runtime-hooks-client.test.ts
index b3ce8dfea..2befccbae 100644
--- a/src/renderer/src/runtime/runtime-hooks-client.test.ts
+++ b/src/renderer/src/runtime/runtime-hooks-client.test.ts
@@ -108,4 +108,35 @@ describe('runtime hooks client', () => {
     expect(hooksReadIssueCommand).not.toHaveBeenCalled()
     expect(hooksWriteIssueCommand).not.toHaveBeenCalled()
   })
+
+  it('forwards an explicit SSH host to local hook IPC', async () => {
+    hooksCheck.mockResolvedValue({ hasHooks: false, hooks: null, mayNeedUpdate: false })
+    hooksReadIssueCommand.mockResolvedValue({
+      localContent: null,
+      sharedContent: null,
+      effectiveContent: null,
+      localFilePath: '',
+      source: 'none'
+    })
+
+    await checkRuntimeHooks({ activeRuntimeEnvironmentId: null }, 'same-repo', 'ssh:server')
+    await readRuntimeIssueCommand({ activeRuntimeEnvironmentId: null }, 'same-repo', 'ssh:server')
+    await writeRuntimeIssueCommand(
+      { activeRuntimeEnvironmentId: null },
+      'same-repo',
+      'Fix it',
+      'ssh:server'
+    )
+
+    expect(hooksCheck).toHaveBeenCalledWith({ repoId: 'same-repo', hostId: 'ssh:server' })
+    expect(hooksReadIssueCommand).toHaveBeenCalledWith({
+      repoId: 'same-repo',
+      hostId: 'ssh:server'
+    })
+    expect(hooksWriteIssueCommand).toHaveBeenCalledWith({
+      repoId: 'same-repo',
+      content: 'Fix it',
+      hostId: 'ssh:server'
+    })
+  })
 })
diff --git a/src/renderer/src/runtime/runtime-hooks-client.ts b/src/renderer/src/runtime/runtime-hooks-client.ts
index eff6f52f5..dc2c884c5 100644
--- a/src/renderer/src/runtime/runtime-hooks-client.ts
+++ b/src/renderer/src/runtime/runtime-hooks-client.ts
@@ -54,11 +54,12 @@ export async function inspectRuntimeSetupScriptImports(
 
 export async function readRuntimeIssueCommand(
   settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined,
-  repoId: string
+  repoId: string,
+  hostId?: ExecutionHostId
 ): Promise<IssueCommandReadResult> {
   const target = getActiveRuntimeTarget(settings)
   if (target.kind !== 'environment') {
-    return window.api.hooks.readIssueCommand({ repoId })
+    return window.api.hooks.readIssueCommand({ repoId, ...(hostId ? { hostId } : {}) })
   }
   return callRuntimeRpc<IssueCommandReadResult>(
     target,
@@ -71,11 +72,12 @@ export async function readRuntimeIssueCommand(
 export async function writeRuntimeIssueCommand(
   settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined,
   repoId: string,
-  content: string
+  content: string,
+  hostId?: ExecutionHostId
 ): Promise<void> {
   const target = getActiveRuntimeTarget(settings)
   if (target.kind !== 'environment') {
-    await window.api.hooks.writeIssueCommand({ repoId, content })
+    await window.api.hooks.writeIssueCommand({ repoId, content, ...(hostId ? { hostId } : {}) })
     return
   }
   await callRuntimeRpc(
diff --git a/src/renderer/src/runtime/runtime-repo-client.test.ts b/src/renderer/src/runtime/runtime-repo-client.test.ts
index 8f0deaaf9..cbd233f0e 100644
--- a/src/renderer/src/runtime/runtime-repo-client.test.ts
+++ b/src/renderer/src/runtime/runtime-repo-client.test.ts
@@ -1,19 +1,26 @@
 // @vitest-environment happy-dom
 
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
-import { searchRuntimeRepoBaseRefDetails, searchRuntimeRepoBaseRefs } from './runtime-repo-client'
+import {
+  getRuntimeRepoBaseRefDefault,
+  searchRuntimeRepoBaseRefDetails,
+  searchRuntimeRepoBaseRefs
+} from './runtime-repo-client'
 
+const getBaseRefDefault = vi.fn()
 const searchBaseRefs = vi.fn()
 const searchBaseRefDetails = vi.fn()
 const runtimeCall = vi.fn()
 
 beforeEach(() => {
+  getBaseRefDefault.mockReset()
   searchBaseRefs.mockReset()
   searchBaseRefDetails.mockReset()
   runtimeCall.mockReset()
   vi.stubGlobal('window', {
     api: {
       repos: {
+        getBaseRefDefault,
         searchBaseRefs,
         searchBaseRefDetails
       },
@@ -51,4 +58,23 @@ describe('runtime repo client search bounds', () => {
     expect(searchBaseRefDetails).not.toHaveBeenCalled()
     expect(runtimeCall).not.toHaveBeenCalled()
   })
+
+  it('forwards the selected SSH host to base-ref IPC', async () => {
+    getBaseRefDefault.mockResolvedValue({ defaultBaseRef: 'origin/main', remoteCount: 1 })
+    searchBaseRefs.mockResolvedValue(['origin/main'])
+
+    await getRuntimeRepoBaseRefDefault(null, 'same-repo', 'ssh:server')
+    await searchRuntimeRepoBaseRefs(null, 'same-repo', 'main', 20, 'ssh:server')
+
+    expect(getBaseRefDefault).toHaveBeenCalledWith({
+      repoId: 'same-repo',
+      hostId: 'ssh:server'
+    })
+    expect(searchBaseRefs).toHaveBeenCalledWith({
+      repoId: 'same-repo',
+      query: 'main',
+      limit: 20,
+      hostId: 'ssh:server'
+    })
+  })
 })
diff --git a/src/renderer/src/runtime/runtime-repo-client.ts b/src/renderer/src/runtime/runtime-repo-client.ts
index 05470c943..6a916d1c6 100644
--- a/src/renderer/src/runtime/runtime-repo-client.ts
+++ b/src/renderer/src/runtime/runtime-repo-client.ts
@@ -2,6 +2,7 @@ import type { BaseRefSearchResult, GlobalSettings } from '../../../shared/types'
 import { legacyBaseRefSearchResult } from '../../../shared/base-ref-search-result'
 import { callRuntimeRpc, getActiveRuntimeTarget } from './runtime-rpc-client'
 import { isRuntimeRepoRefSearchQueryWithinLimit } from './runtime-repo-search-bounds'
+import type { ExecutionHostId } from '../../../shared/execution-host'
 
 export type RuntimeRepoBaseRefDefault = {
   defaultBaseRef: string | null
@@ -10,11 +11,12 @@ export type RuntimeRepoBaseRefDefault = {
 
 export async function getRuntimeRepoBaseRefDefault(
   settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined,
-  repoId: string
+  repoId: string,
+  hostId?: ExecutionHostId
 ): Promise<RuntimeRepoBaseRefDefault> {
   const target = getActiveRuntimeTarget(settings)
   if (target.kind !== 'environment') {
-    return window.api.repos.getBaseRefDefault({ repoId })
+    return window.api.repos.getBaseRefDefault({ repoId, ...(hostId ? { hostId } : {}) })
   }
   return callRuntimeRpc<RuntimeRepoBaseRefDefault>(
     target,
@@ -28,14 +30,15 @@ export async function searchRuntimeRepoBaseRefs(
   settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined,
   repoId: string,
   query: string,
-  limit: number
+  limit: number,
+  hostId?: ExecutionHostId
 ): Promise<string[]> {
   if (!isRuntimeRepoRefSearchQueryWithinLimit(query)) {
     return []
   }
   const target = getActiveRuntimeTarget(settings)
   if (target.kind !== 'environment') {
-    return window.api.repos.searchBaseRefs({ repoId, query, limit })
+    return window.api.repos.searchBaseRefs({ repoId, query, limit, ...(hostId ? { hostId } : {}) })
   }
   const result = await callRuntimeRpc<{ refs: string[]; truncated: boolean }>(
     target,
@@ -50,14 +53,20 @@ export async function searchRuntimeRepoBaseRefDetails(
   settings: Pick<GlobalSettings, 'activeRuntimeEnvironmentId'> | null | undefined,
   repoId: string,
   query: string,
-  limit: number
+  limit: number,
+  hostId?: ExecutionHostId
 ): Promise<BaseRefSearchResult[]> {
   if (!isRuntimeRepoRefSearchQueryWithinLimit(query)) {
     return []
   }
   const target = getActiveRuntimeTarget(settings)
   if (target.kind !== 'environment') {
-    return window.api.repos.searchBaseRefDetails({ repoId, query, limit })
+    return window.api.repos.searchBaseRefDetails({
+      repoId,
+      query,
+      limit,
+      ...(hostId ? { hostId } : {})
+    })
   }
   const result = await callRuntimeRpc<{
     refs: string[]
diff --git a/src/renderer/src/store/slices/repos-host-identity-routing.test.ts b/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
index ebdc85fd4..56d98ca2c 100644
--- a/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
+++ b/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
@@ -133,6 +133,62 @@ describe('repo slice host identity routing', () => {
     )
   })
 
+  it('updateRepo with an explicit hostId routes to that host, not the focused one', async () => {
+    runtimeEnvironmentCall.mockResolvedValue({
+      id: 'rpc-explicit-update',
+      ok: true,
+      result: { repo: { ...remoteDuplicate, displayName: 'Remote via host' } },
+      _meta: { runtimeId: 'runtime-remote' }
+    })
+    const store = createTestStore()
+    // Focus is local (no active runtime env); without the explicit hostId this
+    // would route to the focused (local) row.
+    store.setState({ repos: [localDuplicate, remoteDuplicate] })
+
+    await store
+      .getState()
+      .updateRepo('same-repo', { displayName: 'Remote via host' }, { hostId: 'runtime:env-1' })
+
+    expect(runtimeEnvironmentCall).toHaveBeenCalledWith({
+      selector: 'env-1',
+      method: 'repo.update',
+      params: { repo: 'same-repo', updates: { displayName: 'Remote via host' } },
+      timeoutMs: 15_000
+    })
+    expect(reposUpdate).not.toHaveBeenCalled()
+    expect(store.getState().repos).toEqual([
+      localDuplicate,
+      { ...remoteDuplicate, displayName: 'Remote via host' }
+    ])
+  })
+
+  it('updateRepo with an explicit local hostId stays local even when a runtime is focused', async () => {
+    // The self-pair case: a repo id exists on both local and a focused runtime.
+    // An explicit local hostId must route to local IPC, not the runtime RPC.
+    reposUpdate.mockResolvedValue(undefined)
+    const store = createTestStore()
+    store.setState({
+      settings: { activeRuntimeEnvironmentId: 'env-1' } as never,
+      repos: [localDuplicate, remoteDuplicate]
+    })
+
+    await store
+      .getState()
+      .updateRepo('same-repo', { displayName: 'Local via host' }, { hostId: 'local' })
+
+    expect(reposUpdate).toHaveBeenCalledWith({
+      repoId: 'same-repo',
+      updates: { displayName: 'Local via host' }
+    })
+    expect(runtimeEnvironmentCall).not.toHaveBeenCalledWith(
+      expect.objectContaining({ method: 'repo.update' })
+    )
+    expect(store.getState().repos).toEqual([
+      { ...localDuplicate, displayName: 'Local via host' },
+      remoteDuplicate
+    ])
+  })
+
   it('keeps queued focused-host repo updates pinned when focus changes', async () => {
     const firstUpdate = deferred<{
       id: string
diff --git a/src/renderer/src/store/slices/repos.ts b/src/renderer/src/store/slices/repos.ts
index 45f22711a..165807f27 100644
--- a/src/renderer/src/store/slices/repos.ts
+++ b/src/renderer/src/store/slices/repos.ts
@@ -1497,7 +1497,13 @@ export type RepoSlice = {
   // id exists on multiple hosts; without it the focused host is assumed.
   removeProject: (projectId: string, options?: { hostId?: ExecutionHostId }) => Promise<void>
   updateProject: (projectId: string, updates: ProjectUpdate) => Promise<boolean>
-  updateRepo: (projectId: string, updates: RepoUpdate) => Promise<boolean>
+  // options.hostId targets a specific host's repo row + RPC target when the same
+  // repo id exists on multiple hosts; without it the focused host is assumed.
+  updateRepo: (
+    projectId: string,
+    updates: RepoUpdate,
+    options?: { hostId?: ExecutionHostId }
+  ) => Promise<boolean>
   setActiveRepo: (projectId: string | null) => void
   reorderRepos: (orderedIds: string[]) => Promise<void>
 }
@@ -2978,14 +2984,22 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
     }
   },
 
-  updateRepo: async (projectId, updates) => {
+  updateRepo: async (projectId, updates, options) => {
     const updateRepoChains = getRepoUpdateChains(get)
-    const ownerRepo = findRepoForHost(get().repos, projectId, { settings: get().settings })
+    // Why: pass options.hostId so a duplicate repo id across hosts resolves to the
+    // intended row instead of findRepoForHost's settings-focused fallback.
+    const ownerRepo = findRepoForHost(get().repos, projectId, {
+      settings: get().settings,
+      hostId: options?.hostId
+    })
     if (!ownerRepo) {
       return false
     }
+    // Why: an explicit hostId is authoritative — treat it as an explicit host so
+    // routing goes to that host's target (local IPC or its runtime RPC) rather
+    // than the currently-focused runtime, which is the same-id/self-pair case.
     const ownerHasExplicitHost = Boolean(
-      ownerRepo.executionHostId?.trim() || ownerRepo.connectionId?.trim()
+      options?.hostId || ownerRepo.executionHostId?.trim() || ownerRepo.connectionId?.trim()
     )
     const explicitOwnerHostId = getRepoExecutionHostId(ownerRepo)
     const ownerTarget = ownerHasExplicitHost
diff --git a/src/renderer/src/store/slices/ui.test.ts b/src/renderer/src/store/slices/ui.test.ts
index 6fe4000b4..64c8f0e4a 100644
--- a/src/renderer/src/store/slices/ui.test.ts
+++ b/src/renderer/src/store/slices/ui.test.ts
@@ -984,6 +984,20 @@ describe('createUISlice hydratePersistedUI', () => {
     expect(store.getState().visibleWorkspaceHostIds).toBeNull()
   })
 
+  it('tracks the per-project settings host selection without persisting it', () => {
+    const setUI = vi.fn(() => Promise.resolve())
+    vi.stubGlobal('window', { api: { ui: { set: setUI } } })
+    const store = createUIStore()
+
+    store.getState().setSettingsProjectHostSelection('git:acme/app', 'runtime:home-mac')
+
+    expect(store.getState().settingsProjectHostSelection).toEqual({
+      'git:acme/app': 'runtime:home-mac'
+    })
+    // Ephemeral: never written through the UI persistence pipeline.
+    expect(setUI).not.toHaveBeenCalled()
+  })
+
   it('persists workspace host scope changes', () => {
     const setUI = vi.fn(() => Promise.resolve())
     vi.stubGlobal('window', { api: { ui: { set: setUI } } })
diff --git a/src/renderer/src/store/slices/ui.ts b/src/renderer/src/store/slices/ui.ts
index 5992498c3..26d87bb20 100644
--- a/src/renderer/src/store/slices/ui.ts
+++ b/src/renderer/src/store/slices/ui.ts
@@ -771,6 +771,14 @@ export type UISlice = {
   } | null
   openSettingsTarget: (target: NonNullable<UISlice['settingsNavigationTarget']>) => void
   clearSettingsTarget: () => void
+  /**
+   * Which host the Projects Settings pane shows for each project, keyed by
+   * projectId. Set by the pane's "Available Hosts" switcher. Ephemeral on
+   * purpose — never persisted, so a reload reopens on the project's effective
+   * host rather than a possibly-dangling selection.
+   */
+  settingsProjectHostSelection: Record<string, ExecutionHostId>
+  setSettingsProjectHostSelection: (projectId: string, hostId: ExecutionHostId) => void
   /**
    * One-shot Appearance accordion to expand for nested Settings deep links
    * (e.g. Usage percentages lives under Window & Sidebar). Cleared when
@@ -1533,6 +1541,20 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
   settingsNavigationTarget: null,
   openSettingsTarget: (target) => set({ settingsNavigationTarget: target }),
   clearSettingsTarget: () => set({ settingsNavigationTarget: null }),
+  settingsProjectHostSelection: {},
+  // Why: renderer-only, never persisted — no window.api.ui.set here and this
+  // field is intentionally absent from the debounced UI writer in App.tsx.
+  setSettingsProjectHostSelection: (projectId, hostId) =>
+    set((s) =>
+      s.settingsProjectHostSelection[projectId] === hostId
+        ? s
+        : {
+            settingsProjectHostSelection: {
+              ...s.settingsProjectHostSelection,
+              [projectId]: hostId
+            }
+          }
+    ),
   appearanceAccordionDeepLink: null,
   setAppearanceAccordionDeepLink: (section) => set({ appearanceAccordionDeepLink: section }),
   clearAppearanceAccordionDeepLink: () => set({ appearanceAccordionDeepLink: null }),