Running a Manual Sync

If you need to manually initiate a sync between QuickBooks Desktop and Alternative Payments, you can do so by following these steps.

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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.

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.

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

QuickBooks Desktop syncs must only be initiated from the QBD connector — never from the "Fetch new data" option in the Alternative Payments integrations UI.

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 [e-mail] or reach out via the Live Chat in your partner dashboard.