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Resolving Payout Posting Failures and Invoice Mismatches via Webgility Desktop between Shopify and QuickBooks Desktop

This article helps Webgility Desktop users resolve payout posting errors and discrepancies between Shopify orders and QuickBooks Desktop transactions when using Webgility Desktop. It covers common issues such as mismatched invoices, shipping method conflicts, and failed payout syncs. The guide provides step-by-step instructions to troubleshoot and correct these problems through the Webgility Desktop integration.

Causes of Issues

  • Orders edited in your sales channel are not reflecting properly in QuickBooks.

  • Items removed from the order still appear on posted Invoices.

  • Shipping methods from the sales channel are not mapped correctly in QuickBooks.

  • Payout amounts don’t match between Webgility Desktop and QuickBooks.

Step-by-Step Instructions

1. Update Webgility Desktop

  1. Log in to Webgility Desktop.

  2. Go to Help > Terms and Privacy to check your current version.

  3. Navigate to Help > Check for Updates.

  4. In the Update window, click Update if a new version is available.

  5. Ensure the "Take Webgility database backup" checkbox is selected.

  6. Choose a location to save the backup.

  7. The installer will launch and complete the update.

  8. After installation, log in again to allow the database to update.

  9. Return to Help > Terms and Privacy to confirm the version update.

✅ Webgility Desktop is now up to date!

2. Update Order Download Settings

  • Navigate to:
    Connections > Sales Channel > Settings

  • Under the Order download option:

    • Confirm that order adjustments and order edits are enabled for download.

3. Correct Order-Level Errors

  • Unpost the Order:

    • Go to Posted Orders, locate the affected order, and click Unpost.

  • Edit the Order in Sales Channel:

    • Remove/add items, update shipping, or adjust quantities.

    • Save changes and redownload the order in Webgility Desktop.

  • Post Again to QuickBooks:

    • Post the revised order to reflect accurate details.

  • Fix Invoice Issues:

    • If incorrect items remain on Invoices, manually remove them in QuickBooks or re-sync the corrected order.

4. Fix Mapping or Totals

  • Go to Connections > Shipping > Shipping Method Mapping

    • Confirm that all shipping methods are mapped properly between your sales channel and QuickBooks.

  • Cross-check order totals:

    • Compare order totals, tax, shipping, and discounts in both systems.

    • Make corrections as needed, then re-download the order in Webgility Desktop.

5. Validate Resolution

  • Run a final sync and ensure:

    • Payout is posted correctly

    • Invoices and receipts match order details

    • No discrepancies remain in totals or mapping

    Best Practices

    • Keep Webgility Desktop and QuickBooks up to date.

    • Regularly reconcile posted orders to spot mismatches early.

    • Maintain a log of any manual changes made for audit purposes.