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How to Fix Order Sync Errors from Shopify or Amazon to QuickBooks Desktop via Webgility Desktop

This article helps Webgility Desktop users troubleshoot and resolve order download errors that occur when syncing Shopify or Amazon orders with QuickBooks Desktop through Webgility Desktop. It is intended for scenarios where the issue is not related to QuickBooks Desktop database problems. The guide provides step-by-step instructions to identify and fix common causes of these sync errors.

Overview

You’re assisting a customer who reports that orders from Shopify or Amazon aren’t downloading into QuickBooks Desktop via Webgility Desktop. After confirming there's no database problem, your goal is to check permissions, verify store and QuickBooks Desktop connections, and retry the sync process.

Step-by-Step Troubleshooting

A.  Run Webgility as Administrator

Make sure the customer is running Webgility Desktop with admin rights.

  • Have them right-click the Webgility Desktop shortcut

  • Click “Run as administrator”

  • Confirm that they’re using the latest version of Webgility Desktop

Note: Admin privileges are critical for seamless integration with QuickBooks Desktop

1. Confirm QuickBooks Desktop Connection

Ask the customer to:

  • Open QuickBooks Desktop on the host computer

  • Log in as the Admin user

  • Open the correct company file

Then in Webgility Desktop:

  • Navigate to Connections > Accounting/POS/ERP > Test QuickBooks Desktop Connection

  • Make sure the connection is active and valid

Tip: If QuickBooks Desktop isn’t open or accessible, Webgility won’t be able to sync.

2. Reconnect Shopify and Amazon Stores

In Webgility Desktop:

  • Go to Connections > Sales channels > Manage sales channels

  • Select Shopify and Amazon

  • Click Reconnect or Test Connection

You should see a “connection successful” message for each store.

 Reconnecting ensures that store credentials and tokens are still valid.

3. Retry Downloading Orders

From the Webgility Desktop dashboard:

  • Click Get New Orders for both Shopify and Amazon

  • Watch for new or pending orders to appear in the Order List

 This verifies whether syncing is now working properly.