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How to Resolve Payout Delays Caused by Partial Refunds in Shopify with Webgility Desktop

This article helps Webgility Desktop users investigate and resolve payout delays caused by partially refunded transactions on Shopify-integrated stores. When a refund mismatch occurs between Shopify and Webgility Desktop’s records, the payout may fail to process correctly. The article provides guidance to help support teams identify, isolate, and correct these issues.

Common Symptoms

  • A payout batch appears stuck or delayed in Webgility.

  • The affected order is marked as partially refunded in transaction logs.

  • The refund amount in Webgility does not match Shopify's transaction record.

  • Discrepancies prevent the payout from posting to QuickBooks or completing in Webgility.

Confirming the Issue

1. Review the Payout Log

  • Go to Orders > Shopify >Payoutsin Webgility Desktop.

  • Open the specific pending payout batch.

  • Look for an order that includes a partial refund.

2. Check Transaction History

  • Navigate to Orders > New Orders.

  • Locate the affected order and confirm the refund status.

  • Compare the order total and refund amount within Webgility.

3. Compare With Shopify

  • Log in to the customer’s Shopify admin panel.

  • Open the original order and review the refund history.

  • Confirm whether the refund amount and structure (e.g., item vs. shipping refund) matches what’s recorded in Webgility.

Resolution Procedure

Step 1: Remove the Problematic Order from the Payout Batch

  • In Webgility Desktop, go to Accounting > Payouts.

  • Open the Pending Payout Batch.

  • Click to expand and view the order list.

  • Select the problematic order and choose “Remove from Payout” or the equivalent option.

  • Save the changes.

Step 2: Confirm Payout Completion

  • Re-check the payout batch status.

  • If no further discrepancies are found, the payout should now process and complete successfully.

📌 Note: The removed order will remain excluded from the batch and must be handled separately after reconciling the refund.

Step 3: Verify Shopify Integration Health

  • Go to Connections > Manage Stores.

  • Confirm that the Shopify integration is connected and the sync settings are up to date.

  • If sync issues persist:

    • Perform a manual order sync.

    • Contact Shopify support for clarification on order status or refund behavior.