> For the complete documentation index, see [llms.txt](https://help.alternativepayments.io/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.alternativepayments.io/integrations/accounting-integration-guides/quickbooks-desktop/running-a-manual-sync.md).

# Running a Manual Sync

\*\*\*

{% hint style="info" %}
**Automatic sync:** The connector syncs with QuickBooks Desktop automatically at regular intervals. A manual sync is only needed if you want to push or pull updates immediately.
{% endhint %}

1. **Open your QuickBooks Desktop file.**\
   Make sure you are logged in as an Admin user and in Single-User Mode to ensure all integration permissions are available.
2. **Navigate to the App Management settings.**\
   At the top menu bar, click on: **File** > **App Management** > **Update Web Services.**\
   This will open a new pop-up window that displays the applications connected to your QuickBooks Desktop file.
3. **Find the Alternative Payments application.**\
   In the list of connected applications, locate the **Alternative Payments** application.
4. **Run the manual sync.**\
   Select the checkbox next to the Alternative Payments application, then click **"Update Selected"**.\
   This will manually trigger the sync and push any updates to or from QuickBooks Desktop.
5. **Monitor for confirmation.**\
   After the sync is initiated, progress bars should hit 100% to confirm a successful manual sync.

<figure><img src="https://lh7-rt.googleusercontent.com/docsz/AD_4nXfHWrizrXFERY2Ly2spGJmsxaa0O-e9zKUIhnXobr7O-4jS6LivdYVr4hgfyzs8b2SvrQA_ijoOQgpWbcu2ePrvieC6pGTVT2XKBljnZQzLbO_XsUaKuJyPPDgMND65PbW9z5BRH336Ogvyee9-c2kXU9A?key=UdNZoHXTV0US3C-6i8jsFA" alt=""><figcaption></figcaption></figure>

***

## Important: Do Not Use the AP Platform's "Fetch New Data" Sync for QuickBooks Desktop

{% hint style="warning" %}
**QuickBooks Desktop syncs must only be initiated from the QBD connector — never from the "Fetch new data" option in the Alternative Payments integrations UI.**
{% endhint %}

The Alternative Payments partner dashboard includes a **"Fetch new data"** option in the dropdown menu on your QuickBooks Desktop integration card (under the **Integrations** section). While this option is available for other accounting integrations, it should **not** be used for QuickBooks Desktop.

### Why this matters

For QuickBooks Desktop, the connector itself is the correct and only source of sync triggers. If you use the **"Fetch new data"** option in the AP platform's integrations UI at the same time as the QBD connector is running a sync, the system interprets this as a conflict and initiates a full data backfill. During a backfill, new transactions are placed in a **pre-queued** (on-hold) status to protect data integrity and prevent duplicate records.

Payments stuck in pre-queued status as a result of this dual-trigger scenario are not lost — they can be cleared by running the connector sync manually from within QuickBooks Desktop (via **File > App Management > Update Web Services**). You may need to run the connector sync more than once to fully clear the queue.

### What to do if you have pre-queued payments

If you are seeing payments stuck in a pre-queued status and are unsure of the cause, check whether the **"Fetch new data"** option in the AP platform's integrations UI has been used alongside the QBD connector. This root cause was only recently identified, so partners who experienced unexplained pre-queued payments before mid-2026 may have been affected by this issue without a clear explanation at the time.

**To resolve and prevent this going forward:**

1. Stop using the **"Fetch new data"** option in the AP platform's integrations UI for your QuickBooks Desktop integration.
2. Run the connector sync manually from within QuickBooks Desktop (**File > App Management > Update Web Services > Update Selected**) — repeat if necessary until pre-queued payments clear.
3. Allow the connector to handle all future syncs automatically or manually, as described in the steps above.

If pre-queued payments persist after following these steps, contact our Customer Experience team at <customersuccess@alternativepayments.io> or reach out via the Live Chat in your partner dashboard.


---

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