diff --git a/packages/frontend/apps/electron-renderer/src/app/setup.ts b/packages/frontend/apps/electron-renderer/src/app/setup.ts
index 99d145d296..8c0efdd221 100644
--- a/packages/frontend/apps/electron-renderer/src/app/setup.ts
+++ b/packages/frontend/apps/electron-renderer/src/app/setup.ts
@@ -1,5 +1,6 @@
 import '@affine/core/bootstrap/electron';
 import '@affine/core/bootstrap/blocksuite';
+import '@affine/core/bootstrap/cleanup';
 import '@affine/component/theme';
 import './global.css';
 
diff --git a/packages/frontend/apps/ios/src/setup.ts b/packages/frontend/apps/ios/src/setup.ts
index cc5cf55bad..037cf5c436 100644
--- a/packages/frontend/apps/ios/src/setup.ts
+++ b/packages/frontend/apps/ios/src/setup.ts
@@ -1,3 +1,4 @@
 import '@affine/core/bootstrap/browser';
 import '@affine/core/bootstrap/blocksuite';
+import '@affine/core/bootstrap/cleanup';
 import './proxy';
diff --git a/packages/frontend/apps/mobile/src/setup.ts b/packages/frontend/apps/mobile/src/setup.ts
index 64569a71e2..91115ee8c5 100644
--- a/packages/frontend/apps/mobile/src/setup.ts
+++ b/packages/frontend/apps/mobile/src/setup.ts
@@ -1,4 +1,5 @@
 import '@affine/core/bootstrap/browser';
 import '@affine/core/bootstrap/blocksuite';
+import '@affine/core/bootstrap/cleanup';
 import '@affine/component/theme';
 import '@affine/core/mobile/styles/mobile.css';
diff --git a/packages/frontend/apps/web/src/setup.ts b/packages/frontend/apps/web/src/setup.ts
index 76e2660119..765f04e23d 100644
--- a/packages/frontend/apps/web/src/setup.ts
+++ b/packages/frontend/apps/web/src/setup.ts
@@ -1,3 +1,4 @@
 import '@affine/core/bootstrap/browser';
 import '@affine/core/bootstrap/blocksuite';
+import '@affine/core/bootstrap/cleanup';
 import '@affine/component/theme';
diff --git a/packages/frontend/core/src/bootstrap/cleanup.ts b/packages/frontend/core/src/bootstrap/cleanup.ts
new file mode 100644
index 0000000000..d97ab165f6
--- /dev/null
+++ b/packages/frontend/core/src/bootstrap/cleanup.ts
@@ -0,0 +1,28 @@
+function cleanupUnusedIndexedDB() {
+  const indexedDB = window.indexedDB;
+  if (!indexedDB) {
+    return;
+  }
+
+  indexedDB.databases().then(databases => {
+    databases.forEach(database => {
+      if (database.name?.endsWith(':server-clock')) {
+        indexedDB.deleteDatabase(database.name);
+      }
+      if (database.name?.endsWith(':sync-metadata')) {
+        indexedDB.deleteDatabase(database.name);
+      }
+      if (
+        database.name?.startsWith('idx:') &&
+        (database.name.endsWith(':block') || database.name.endsWith(':doc'))
+      ) {
+        indexedDB.deleteDatabase(database.name);
+      }
+      if (database.name?.startsWith('jp:')) {
+        indexedDB.deleteDatabase(database.name);
+      }
+    });
+  });
+}
+
+cleanupUnusedIndexedDB();