diff --git a/packages/common/nbstore/src/impls/idb/indexer-sync.ts b/packages/common/nbstore/src/impls/idb/indexer-sync.ts
index 690fa86078..5d0faf4f8b 100644
--- a/packages/common/nbstore/src/impls/idb/indexer-sync.ts
+++ b/packages/common/nbstore/src/impls/idb/indexer-sync.ts
@@ -1,6 +1,8 @@
 import { share } from '../../connection';
-import type { DocClock } from '../../storage/doc';
-import { IndexerSyncStorageBase } from '../../storage/indexer-sync';
+import {
+  type DocIndexedClock,
+  IndexerSyncStorageBase,
+} from '../../storage/indexer-sync';
 import { IDBConnection, type IDBConnectionOptions } from './db';
 
 export class IndexedDBIndexerSyncStorage extends IndexerSyncStorageBase {
@@ -12,21 +14,26 @@ export class IndexedDBIndexerSyncStorage extends IndexerSyncStorageBase {
     super();
   }
 
-  async getDocIndexedClock(docId: string): Promise<DocClock | null> {
+  async getDocIndexedClock(docId: string): Promise<DocIndexedClock | null> {
     const tx = this.connection.inner.db.transaction('indexerSync', 'readonly');
     const store = tx.store;
     const result = await store.get(docId);
     return result
-      ? { docId: result.docId, timestamp: result.indexedClock }
+      ? {
+          docId: result.docId,
+          timestamp: result.indexedClock,
+          indexerVersion: result.indexerVersion ?? 0,
+        }
       : null;
   }
 
-  async setDocIndexedClock(docClock: DocClock): Promise<void> {
+  async setDocIndexedClock(docClock: DocIndexedClock): Promise<void> {
     const tx = this.connection.inner.db.transaction('indexerSync', 'readwrite');
     const store = tx.store;
     await store.put({
       docId: docClock.docId,
       indexedClock: docClock.timestamp,
+      indexerVersion: docClock.indexerVersion,
     });
   }
 
diff --git a/packages/common/nbstore/src/impls/idb/schema.ts b/packages/common/nbstore/src/impls/idb/schema.ts
index 35e206c2cb..a27cf6fce5 100644
--- a/packages/common/nbstore/src/impls/idb/schema.ts
+++ b/packages/common/nbstore/src/impls/idb/schema.ts
@@ -38,9 +38,9 @@ Table(PeerClocks)
 | str  |  str  |   Date    |   Date    |
 
 Table(IndexerSync)
-| docId | clock |
-|-------|-------|
-| str   | Date  |
+| docId | indexedClock | indexerVersion |
+|-------|--------------|----------------|
+| str   |   Date       |    number      |
 
 Table(BlobSync)
 | peer | key | uploadedAt |
@@ -134,6 +134,7 @@ export interface DocStorageSchema extends DBSchema {
     value: {
       docId: string;
       indexedClock: Date;
+      indexerVersion?: number;
     };
   };
   indexerMetadata: {
diff --git a/packages/common/nbstore/src/storage/dummy/indexer-sync.ts b/packages/common/nbstore/src/storage/dummy/indexer-sync.ts
index 96ec17f744..a3adcf73cd 100644
--- a/packages/common/nbstore/src/storage/dummy/indexer-sync.ts
+++ b/packages/common/nbstore/src/storage/dummy/indexer-sync.ts
@@ -1,13 +1,12 @@
 import { DummyConnection } from '../../connection';
-import type { DocClock } from '../doc';
-import { IndexerSyncStorageBase } from '../indexer-sync';
+import { type DocIndexedClock, IndexerSyncStorageBase } from '../indexer-sync';
 
 export class DummyIndexerSyncStorage extends IndexerSyncStorageBase {
   override connection = new DummyConnection();
-  override getDocIndexedClock(_docId: string): Promise<DocClock | null> {
+  override getDocIndexedClock(_docId: string): Promise<DocIndexedClock | null> {
     return Promise.resolve(null);
   }
-  override setDocIndexedClock(_docClock: DocClock): Promise<void> {
+  override setDocIndexedClock(_docClock: DocIndexedClock): Promise<void> {
     return Promise.resolve();
   }
   override clearDocIndexedClock(_docId: string): Promise<void> {
diff --git a/packages/common/nbstore/src/storage/indexer-sync.ts b/packages/common/nbstore/src/storage/indexer-sync.ts
index 8be6c8b5d3..3cb8168294 100644
--- a/packages/common/nbstore/src/storage/indexer-sync.ts
+++ b/packages/common/nbstore/src/storage/indexer-sync.ts
@@ -2,12 +2,16 @@ import type { Connection } from '../connection';
 import type { DocClock } from './doc';
 import type { Storage } from './storage';
 
+export interface DocIndexedClock extends DocClock {
+  indexerVersion: number;
+}
+
 export interface IndexerSyncStorage extends Storage {
   readonly storageType: 'indexerSync';
 
-  getDocIndexedClock(docId: string): Promise<DocClock | null>;
+  getDocIndexedClock(docId: string): Promise<DocIndexedClock | null>;
 
-  setDocIndexedClock(docClock: DocClock): Promise<void>;
+  setDocIndexedClock(docClock: DocIndexedClock): Promise<void>;
 
   clearDocIndexedClock(docId: string): Promise<void>;
 }
@@ -15,7 +19,7 @@ export interface IndexerSyncStorage extends Storage {
 export abstract class IndexerSyncStorageBase implements IndexerSyncStorage {
   readonly storageType = 'indexerSync';
   abstract connection: Connection<any>;
-  abstract getDocIndexedClock(docId: string): Promise<DocClock | null>;
-  abstract setDocIndexedClock(docClock: DocClock): Promise<void>;
+  abstract getDocIndexedClock(docId: string): Promise<DocIndexedClock | null>;
+  abstract setDocIndexedClock(docClock: DocIndexedClock): Promise<void>;
   abstract clearDocIndexedClock(docId: string): Promise<void>;
 }
diff --git a/packages/common/nbstore/src/sync/indexer/index.ts b/packages/common/nbstore/src/sync/indexer/index.ts
index ff453f54ee..55d6a50b74 100644
--- a/packages/common/nbstore/src/sync/indexer/index.ts
+++ b/packages/common/nbstore/src/sync/indexer/index.ts
@@ -65,6 +65,10 @@ export interface IndexerSync {
 }
 
 export class IndexerSyncImpl implements IndexerSync {
+  /**
+   * increase this number to re-index all docs
+   */
+  readonly INDEXER_VERSION = 1;
   private abort: AbortController | null = null;
   private readonly rootDocId = this.doc.spaceId;
   private readonly status = new IndexerSyncStatus(this.rootDocId);
@@ -351,7 +355,9 @@ export class IndexerSyncImpl implements IndexerSync {
             await this.indexerSync.getDocIndexedClock(docId);
           if (
             docIndexedClock &&
-            docIndexedClock.timestamp.getTime() === docClock.timestamp.getTime()
+            docIndexedClock.timestamp.getTime() ===
+              docClock.timestamp.getTime() &&
+            docIndexedClock.indexerVersion === this.INDEXER_VERSION
           ) {
             // doc is already indexed, just skip
             continue;
@@ -406,6 +412,7 @@ export class IndexerSyncImpl implements IndexerSync {
           await this.indexerSync.setDocIndexedClock({
             docId,
             timestamp: docClock.timestamp,
+            indexerVersion: this.INDEXER_VERSION,
           });
           // #endregion
         }