diff --git a/src/renderer/src/store/slices/worktrees.test.ts b/src/renderer/src/store/slices/worktrees.test.ts
index 9c03c0ca5..4f8587db4 100644
--- a/src/renderer/src/store/slices/worktrees.test.ts
+++ b/src/renderer/src/store/slices/worktrees.test.ts
@@ -7156,6 +7156,34 @@ describe('markWorktreeVisited', () => {
     })
   })
 
+  it('pruneLastVisitedTimestamps clears a stale activeWorktreeId gone from a hydrated repo', () => {
+    const store = createTestStore()
+    const wt = makeWorktree({ id: 'repo1::/a', repoId: 'repo1', path: '/a' })
+    store.setState({
+      worktreesByRepo: { repo1: [wt] },
+      activeWorktreeId: 'repo1::/gone',
+      lastVisitedAtByWorktreeId: {}
+    } as Partial<AppState>)
+    store.getState().pruneLastVisitedTimestamps()
+    expect(store.getState().activeWorktreeId).toBeNull()
+  })
+
+  it('pruneLastVisitedTimestamps keeps a live activeWorktreeId and defers unhydrated repos', () => {
+    const store = createTestStore()
+    const wt = makeWorktree({ id: 'repo1::/a', repoId: 'repo1', path: '/a' })
+    store.setState({
+      worktreesByRepo: { repo1: [wt] },
+      activeWorktreeId: 'repo1::/a'
+    } as Partial<AppState>)
+    store.getState().pruneLastVisitedTimestamps()
+    expect(store.getState().activeWorktreeId).toBe('repo1::/a')
+
+    // A pointer into a not-yet-hydrated (e.g. SSH pre-connect) repo is deferred.
+    store.setState({ activeWorktreeId: 'ssh-repo::/b' } as Partial<AppState>)
+    store.getState().pruneLastVisitedTimestamps()
+    expect(store.getState().activeWorktreeId).toBe('ssh-repo::/b')
+  })
+
   it('pruneLastVisitedTimestamps defers when the detected list is non-authoritative', () => {
     const store = createTestStore()
     store.setState({
diff --git a/src/renderer/src/store/slices/worktrees.ts b/src/renderer/src/store/slices/worktrees.ts
index ca00a12e5..b10674821 100644
--- a/src/renderer/src/store/slices/worktrees.ts
+++ b/src/renderer/src/store/slices/worktrees.ts
@@ -4428,7 +4428,27 @@ export const createWorktreeSlice: StateCreator<AppState, [], [], WorktreeSlice>
           changed = true
         }
       }
-      return changed ? { lastVisitedAtByWorktreeId: next } : {}
+      const patch: { lastVisitedAtByWorktreeId?: Record<string, number>; activeWorktreeId?: null } =
+        {}
+      if (changed) {
+        patch.lastVisitedAtByWorktreeId = next
+      }
+      // Why: the persisted active-worktree pointer is a `${repoId}::${path}` id
+      // that nothing else reconciles here. The main-process Store clears a stale
+      // pointer when a repo is removed (removeWorkspaceSessionOwner nulls
+      // activeWorktreeId), but the web client keeps it in localStorage and gets
+      // no such load-time GC — so a pointer to a worktree the server no longer
+      // reports lingers and can surface a phantom/duplicate workspace. Clear it
+      // once its repo is hydrated and the worktree is confirmed gone (defer while
+      // the repo is unhydrated, mirroring the timestamp rule above).
+      const activeId = s.activeWorktreeId
+      if (activeId) {
+        const activeRepoWorktreeIds = validIdsByRepo.get(getRepoIdFromWorktreeId(activeId))
+        if (activeRepoWorktreeIds && !activeRepoWorktreeIds.has(activeId)) {
+          patch.activeWorktreeId = null
+        }
+      }
+      return Object.keys(patch).length > 0 ? patch : {}
     })
   },