Fix Shopify Orders Marked as Paid After an Order Update in Webgility Desktop

Intro

If an edited Shopify order is unexpectedly marked as Paid after being posted to QuickBooks Online, QuickBooks Online may have automatically applied an existing customer credit to the invoice.

Learn how to prevent this and correctly re-post the updated order.

Causes of Issues

This issue can occur when:

• Automatically apply credits is enabled in QuickBooks Online.
• QuickBooks Online applies an existing customer credit to the invoice created or updated by Webgility.
• Webgility detects the invoice as paid and syncs the payment status back to Shopify.

Step-by-Step Instructions

1. Turn off automatic credit application in QuickBooks Online.

Navigate to Settings ⚙️ > Account and settings > Advanced > Automation.

Turn off Automatically apply credits, then select Save and Done.

This prevents QuickBooks Online from automatically applying existing customer credits to newly created or updated invoices.

Note: This setting affects customer transactions in QuickBooks Online, not only Shopify orders. Make sure disabling it will not affect your other accounting workflows.

2. Accept the updated Shopify order in Webgility Desktop.

When the edited order appears in the Updates tab:

• Select the order.
• Select Accept.
• When prompted that accepting the changes will un-post the existing transaction, select Yes.

The order will move back to New Orders so it can be posted again with the updated information.

For detailed instructions, see How to Accept Updates for Orders in Webgility Desktop. 

3. Re-post the order.

Go to New Orders and post the updated Shopify order to QuickBooks Online.

For more information about syncing payment status between QuickBooks Online and Shopify, see Sync Payment Status for Orders from QuickBooks to Shopify Using Webgility Desktop.

4. Verify the order status.

After posting:

• Check QuickBooks Online and confirm the invoice remains unpaid until an actual payment is received.
• Check Shopify and confirm the order is no longer being automatically marked as Paid.

Notes

If the order continues to be marked as paid after automatic credit application is disabled, check the QuickBooks Online customer transaction history for any payment or credit applied to the invoice.

If the issue persists, contact Webgility Support with:

• Shopify order number
• QuickBooks Online invoice number
• Screenshot of the QuickBooks Online transaction history

This information will help Support identify what is causing the payment status to change.