diff --git a/modules/module-mongodb-storage/src/storage/implementation/MongoBucketBatch.ts b/modules/module-mongodb-storage/src/storage/implementation/MongoBucketBatch.ts
index 01e7b6497..6ad06a327 100644
--- a/modules/module-mongodb-storage/src/storage/implementation/MongoBucketBatch.ts
+++ b/modules/module-mongodb-storage/src/storage/implementation/MongoBucketBatch.ts
@@ -133,7 +133,7 @@ export class MongoBucketBatch
     let result: storage.FlushedResult | null = null;
     // One flush may be split over multiple transactions.
     // Each flushInner() is one transaction.
-    while (this.batch != null) {
+    while (this.batch != null || this.write_checkpoint_batch.length > 0) {
       let r = await this.flushInner(options);
       if (r) {
         result = r;
@@ -144,17 +144,16 @@ export class MongoBucketBatch
 
   private async flushInner(options?: storage.BatchBucketFlushOptions): Promise<storage.FlushedResult | null> {
     const batch = this.batch;
-    if (batch == null) {
-      return null;
-    }
-
     let last_op: InternalOpId | null = null;
     let resumeBatch: OperationBatch | null = null;
 
-    await this.withReplicationTransaction(`Flushing ${batch.length} ops`, async (session, opSeq) => {
-      resumeBatch = await this.replicateBatch(session, batch, opSeq, options);
+    await this.withReplicationTransaction(`Flushing ${batch?.length ?? 0} ops`, async (session, opSeq) => {
+      if (batch != null) {
+        resumeBatch = await this.replicateBatch(session, batch, opSeq, options);
+      }
 
       if (this.write_checkpoint_batch.length > 0) {
+        this.logger.info(`Writing ${this.write_checkpoint_batch.length} custom write checkpoints`);
         await batchCreateCustomWriteCheckpoints(this.db, session, this.write_checkpoint_batch, opSeq.next());
         this.write_checkpoint_batch = [];
       }
diff --git a/packages/service-core-tests/src/tests/register-data-storage-tests.ts b/packages/service-core-tests/src/tests/register-data-storage-tests.ts
index e8ff90fdb..a766fef47 100644
--- a/packages/service-core-tests/src/tests/register-data-storage-tests.ts
+++ b/packages/service-core-tests/src/tests/register-data-storage-tests.ts
@@ -1790,6 +1790,50 @@ bucket_definitions:
     });
   });
 
+  test('custom write checkpoints - standalone checkpoint', async (context) => {
+    await using factory = await generateStorageFactory();
+    const r = await factory.configureSyncRules({
+      content: `
+bucket_definitions:
+  mybucket:
+    data: []
+    `,
+      validate: false
+    });
+    const bucketStorage = factory.getInstance(r.persisted_sync_rules!);
+    await bucketStorage.autoActivate();
+    bucketStorage.setWriteCheckpointMode(storage.WriteCheckpointMode.CUSTOM);
+
+    const abortController = new AbortController();
+    context.onTestFinished(() => abortController.abort());
+    const iter = bucketStorage
+      .watchCheckpointChanges({ user_id: 'user1', signal: abortController.signal })
+      [Symbol.asyncIterator]();
+
+    await bucketStorage.startBatch(test_utils.BATCH_OPTIONS, async (batch) => {
+      // Flush to clear state
+      await batch.flush();
+
+      await batch.addCustomWriteCheckpoint({
+        checkpoint: 5n,
+        user_id: 'user1'
+      });
+      await batch.flush();
+      await batch.keepalive('5/0');
+    });
+
+    const result = await iter.next();
+    expect(result).toMatchObject({
+      done: false,
+      value: {
+        base: {
+          lsn: '5/0'
+        },
+        writeCheckpoint: 5n
+      }
+    });
+  });
+
   test('custom write checkpoints - write after checkpoint', async (context) => {
     await using factory = await generateStorageFactory();
     const r = await factory.configureSyncRules({