diff --git a/apps/electron/src/helper/db/base-db-adapter.ts b/apps/electron/src/helper/db/base-db-adapter.ts
index 7d90c8a0bb..44f5669b88 100644
--- a/apps/electron/src/helper/db/base-db-adapter.ts
+++ b/apps/electron/src/helper/db/base-db-adapter.ts
@@ -1,5 +1,10 @@
-import { type InsertRow, SqliteConnection } from '@affine/native';
+import {
+  type InsertRow,
+  SqliteConnection,
+  ValidationResult,
+} from '@affine/native';
 
+import { migrateToLatestDatabase } from '../db/migration';
 import { logger } from '../logger';
 
 /**
@@ -13,6 +18,10 @@ export abstract class BaseSQLiteAdapter {
 
   async connectIfNeeded() {
     if (!this.db) {
+      const validation = await SqliteConnection.validate(this.path);
+      if (validation === ValidationResult.MissingVersionColumn) {
+        await migrateToLatestDatabase(this.path);
+      }
       this.db = new SqliteConnection(this.path);
       await this.db.connect();
       logger.info(`[SQLiteAdapter:${this.role}]`, 'connected:', this.path);
diff --git a/packages/workspace/src/local/crud.ts b/packages/workspace/src/local/crud.ts
index 498a0837f8..9594eaa30c 100644
--- a/packages/workspace/src/local/crud.ts
+++ b/packages/workspace/src/local/crud.ts
@@ -98,10 +98,17 @@ export const CRUD: WorkspaceCRUD<WorkspaceFlavour.LOCAL> = {
   list: async () => {
     logger.debug('list');
     const storage = getStorage();
-    const allWorkspaceIDs: string[] = storage.getItem(kStoreKey, []) as z.infer<
+    let allWorkspaceIDs: string[] = storage.getItem(kStoreKey, []) as z.infer<
       typeof schema
     >;
 
+    // fixme: remove this once desktop data migration is done
+    if (window.apis && environment.isDesktop) {
+      const desktopIds = (await window.apis.workspace.list()).map(v => v[0]);
+      allWorkspaceIDs = [...new Set([...allWorkspaceIDs, ...desktopIds])];
+      storage.setItem(kStoreKey, allWorkspaceIDs);
+    }
+
     const workspaces = (
       await Promise.all(allWorkspaceIDs.map(id => CRUD.get(id)))
     ).filter(item => item !== null) as LocalWorkspace[];