Skip to content
  • There are no suggestions because the search field is empty.

How to Fix Shopify Connection Issues and Payout Mismatches in QuickBooks via Webgility Desktop

This article helps Webgility Desktop users in addressing issues arising from Shopify system updates that disrupt Webgility Desktop integration and cause payout mismatches with QuickBooks Desktop. It focuses on resolving problems related to API changes requiring Webgility Desktop updates, discrepancies between Shopify payout reports and invoices in QuickBooks Desktop, and missing invoice numbers in Shopify data.

This article provides a step-by-step solution for addressing Shopify system updates that disrupt Webgility integration and cause payout mismatches with QuickBooks, specifically due to API changes and missing invoice numbers.

Causes: 

  • Shopify requires Webgility to be updated and reconnected due to API changes.
  • Payout reports from Shopify on a specific date do not match invoices in QuickBooks.
  • Missing invoice numbers in Shopify data cause payout mismatches.

Resolution Steps

1. Update Webgility Software:

Navigate to Help > Check for Updates.
Check the box labeled "Take Webgility database backup before proceeding with the update." Click Update.

You’ll be prompted to choose a folder to save the Webgility database backup.
Once the folder is selected, the application will proceed to update Webgility to the latest version. You can also follow the steps of the following help article to complete the update process: Help Article.

2. Reconnect Shopify Store in Webgility:

  • Navigate to Connections > Sales Channel > Manage Sales Channel in Webgility.
  • Click on the Action button next to your store and then TEST THE CONNECTION.
  • Follow the OAuth sequence in Shopify to grant the necessary permissions.

3. Redownload the payout and try posting again:

Follow the steps given in the following help article to redownload the payout report: Help Article.

Once the payout has been redownloaded successfully, please try posting again.