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How to Resolve Common Errors When Posting Shopify Payouts to QuickBooks Desktop

This article helps Webgility Desktop users troubleshoot and resolve common issues encountered when posting Shopify payouts to QuickBooks Desktop via Webgility Desktop. It covers scenarios such as pending payouts, posting errors, missing transactions, and reconciliation mismatches, providing step-by-step guidance to ensure accurate and successful payout posting.

Common Issues

Webgility users may encounter the following issues when processing Shopify payouts:

  • Payouts stuck in Pending or Failed status

  • Error messages during payout posting or reconciliation

  • Payouts missing from QuickBooks or bank feeds

  • Duplicate or mismatched invoices

  • Manual adjustments needed to complete reconciliation

Step-by-Step Troubleshooting Guide

1. Check Payout Status in Shopify

  1. Log in to your Shopify Admin.

  2. Navigate to Settings > Payments > Payouts.

  3. Review the status of the payout:

    • Paid – processed and deposited

    • Pending – scheduled, but not yet processed

    • Failed – issue encountered during transfer

Record the Payout ID for use in later troubleshooting.

2. Review Error Logs in Webgility

  1. Open Webgility Desktop.

  2. Go to Accounting > Payouts and locate the failed payout.

  3. Click View Error Log to identify issues such as:

    • Invalid or outdated bank account info

    • Orders not yet synced or posted to QuickBooks

    • API connection issues with Shopify or QuickBooks

If order errors are found, refer to the Order Sync Troubleshooting Guide for steps to resolve them.

3. Handle Failed or Mis-Posted Payouts

In Shopify:

  • Use “Mark as Paid” or “Retry Payout” if applicable.

In QuickBooks:

  • If the payout was not posted:

    • Manually record the transaction, or

    • Re-post it using Webgility once underlying issues are resolved.

In Webgility:

  • Confirm all related orders, refunds, and fees are posted.

  • Use the Payout Reconciliation Tool to review line item accuracy.

4. Fix Invoice or Reconciliation Discrepancies

  1. In Webgility, review orders linked to the payout.

  2. Audit each order/invoice in QuickBooks for:

    • Missing line items

    • Incorrect taxes or payment methods

    • Duplicate entries (from re-downloaded orders)

Important: If you need to re-download orders, first Unsync them in Webgility to avoid duplicates in QuickBooks.

  1. Correct discrepancies directly in Shopify or QuickBooks as needed.

  2. Re-run the sync or payout posting process from Webgility.

Best Practices for Payout Accuracy

  • Use Webgility’s Payout Reconciliation Tool regularly.

  • Perform monthly reconciliations between Shopify and QuickBooks.

  • Enable error notifications in Webgility to catch sync failures early.

  • Always Unsync orders before re-downloading them to avoid duplication.