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How to Resolve Shopify Sync and Invoice Reconciliation Issues

This article helps Webgility Desktop users troubleshoot and resolve Shopify sales channel connection errors and invoice reconciliation discrepancies in QuickBooks Online posted through Webgility Online. It provides a step-by-step guide to effectively address these common issues and ensure smooth data synchronization.

Causes of Issues:

  • API Credential Errors: Incorrect or outdated API credentials may block sync operations.

  • Permission Mismatch: Missing permissions on Shopify can prevent data sync.

  • Manual Tax Adjustments: If taxes are adjusted manually in QuickBooks, invoice totals may not match order totals.

Steps to Resolve Shopify Sync and Invoice Reconciliation Issues:

1. Reconnect Shopify Sales channel connection

  • Go to the Webgility Online Dashboard:
    Navigate to Connections > Sales Channel > Reauthorization and re-authenticate your sales channel to refresh the connection.

2. Synchronize Data Manually

  • Navigate to Sync Settings > Products in Webgility Online.

  • On each tab, locate and click the Refresh Settings option to begin downloading the latest data and settings from QuickBooks.

  • Under both the Product and Customer tabs, use the drop-down menu to select either:

    • Refresh Latest Accounting Data – updates recent changes.

    • Download from Scratch – redownloads all products and customer data (recommended if recent changes are not reflected).

  • Click Refresh Settings to initiate the download process.

  • Wait a few minutes for the download to complete, especially if you have a large dataset in QuickBooks.

  • Once the process is complete, a notification will confirm that the data has been successfully downloaded. 

3. Locate and Reconcile Invoices

  • Navigate to:Sales > Orders

  • Use filters to locate specific orders with discrepancies.

  • Check if invoice amounts differ due to tax, discounts, or manual changes.

  • Confirm that the invoice totals match the Shopify order totals.

4. Adjust Payment Posting Settings

  • Go to: Sync Settings > Orders

  • Under Order Settings, verify whether you're posting payment under correct accounts.

  • Adjust the setting to match your reconciliation workflow.

Note: If the order total includes tax collected by Shopify or Avalara, but the QuickBooks invoice does not reflect the same, it may result in mismatch and payment posting issues. Ensure consistent tax mapping across systems.

Additional Tip: You can use screenshots or sample transactions when the sync and reconciliation worked correctly to compare and identify what’s changed.