diff --git a/apps/desktop/src/stores/savedSqlStore.ts b/apps/desktop/src/stores/savedSqlStore.ts
index 0b659676f..a08be5db8 100644
--- a/apps/desktop/src/stores/savedSqlStore.ts
+++ b/apps/desktop/src/stores/savedSqlStore.ts
@@ -13,6 +13,16 @@ interface SavedSqlState {
   files: SavedSqlFile[];
 }
 
+interface SaveFileInput {
+  id?: string;
+  connectionId: string;
+  folderId?: string;
+  name: string;
+  database: string;
+  schema?: string;
+  sql: string;
+}
+
 function nowIso() {
   return new Date().toISOString();
 }
@@ -206,13 +216,16 @@ export const useSavedSqlStore = defineStore("savedSql", () => {
     await syncToLocalDirectory();
   }
 
-  async function saveFile(input: { id?: string; connectionId: string; folderId?: string; name: string; database: string; schema?: string; sql: string }) {
+  async function saveFile(input: SaveFileInput) {
     const timestamp = nowIso();
     const existing = input.id ? getFile(input.id) : undefined;
+    const hasFolderIdInput = Object.prototype.hasOwnProperty.call(input, "folderId");
     const file: SavedSqlFile = existing
       ? {
           ...existing,
-          folderId: input.folderId || undefined,
+          // Partial metadata updates should not move files out of their folder.
+          // Callers that intentionally move to root pass `folderId: undefined`.
+          folderId: hasFolderIdInput ? input.folderId || undefined : existing.folderId,
           name: input.name,
           database: input.database,
           schema: input.schema,
diff --git a/packages/app-tests/savedSqlStore.test.ts b/packages/app-tests/savedSqlStore.test.ts
index b322e4b49..eb547bd8a 100644
--- a/packages/app-tests/savedSqlStore.test.ts
+++ b/packages/app-tests/savedSqlStore.test.ts
@@ -8,6 +8,7 @@ const apiMock = vi.hoisted(() => ({
   loadSavedSqlLibrary: vi.fn<() => Promise<SavedSqlLibrary>>(),
   loadSavedSqlFile: vi.fn<(id: string) => Promise<SavedSqlFile | null>>(),
   saveSavedSqlFolder: vi.fn<(folder: SavedSqlFolder) => Promise<SavedSqlFolder>>(),
+  saveSavedSqlFile: vi.fn<(file: SavedSqlFile) => Promise<SavedSqlFile>>(),
   syncSavedSqlDirectory: vi.fn<() => Promise<void>>(),
 }));
 
@@ -18,6 +19,7 @@ beforeEach(() => {
   apiMock.loadSavedSqlLibrary.mockResolvedValue({ folders: [], files: [] });
   apiMock.loadSavedSqlFile.mockResolvedValue(null);
   apiMock.saveSavedSqlFolder.mockImplementation(async (folder) => folder);
+  apiMock.saveSavedSqlFile.mockImplementation(async (file) => file);
   apiMock.syncSavedSqlDirectory.mockResolvedValue();
   vi.clearAllMocks();
 });
@@ -72,3 +74,64 @@ test("saved SQL summaries load file content on demand", async () => {
   assert.equal(store.files[0]?.sql, "SELECT 1;");
   assert.equal(apiMock.loadSavedSqlFile.mock.calls.length, 1);
 });
+
+test("saving an existing SQL file without folderId keeps its folder", async () => {
+  const file: SavedSqlFile = {
+    id: "sql-1",
+    connectionId: "conn-1",
+    folderId: "folder-1",
+    name: "query.sql",
+    database: "db",
+    sql: "SELECT 1;",
+    sqlLoaded: true,
+    createdAt: "2026-06-27T00:00:00.000Z",
+    updatedAt: "2026-06-27T00:00:00.000Z",
+  };
+  apiMock.loadSavedSqlLibrary.mockResolvedValue({ folders: [], files: [file] });
+
+  const store = useSavedSqlStore();
+  await store.initFromStorage();
+
+  const saved = await store.saveFile({
+    id: "sql-1",
+    connectionId: "conn-2",
+    name: "query.sql",
+    database: "other_db",
+    sql: "SELECT 1;",
+  });
+
+  assert.equal(saved.folderId, "folder-1");
+  assert.equal(apiMock.saveSavedSqlFile.mock.calls[0]?.[0].folderId, "folder-1");
+  assert.equal(store.getFile("sql-1")?.folderId, "folder-1");
+});
+
+test("saving an existing SQL file with root folder explicitly moves it to root", async () => {
+  const file: SavedSqlFile = {
+    id: "sql-1",
+    connectionId: "conn-1",
+    folderId: "folder-1",
+    name: "query.sql",
+    database: "db",
+    sql: "SELECT 1;",
+    sqlLoaded: true,
+    createdAt: "2026-06-27T00:00:00.000Z",
+    updatedAt: "2026-06-27T00:00:00.000Z",
+  };
+  apiMock.loadSavedSqlLibrary.mockResolvedValue({ folders: [], files: [file] });
+
+  const store = useSavedSqlStore();
+  await store.initFromStorage();
+
+  const saved = await store.saveFile({
+    id: "sql-1",
+    connectionId: "conn-1",
+    folderId: undefined,
+    name: "query.sql",
+    database: "db",
+    sql: "SELECT 1;",
+  });
+
+  assert.equal(saved.folderId, undefined);
+  assert.equal(apiMock.saveSavedSqlFile.mock.calls[0]?.[0].folderId, undefined);
+  assert.equal(store.getFile("sql-1")?.folderId, undefined);
+});