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Troubleshooting Incorrect Shopify Payout Entries Synced via Webgility Desktop

This article helps Webgility Desktop users in resolving issues where Shopify payouts are not syncing correctly into QuickBooks Desktop through Webgility Desktop. These issues may include missing, incorrect, or duplicate payout entries, typically resulting from sync mismatches or connectivity disruptions between Shopify and QuickBooks Desktop. The article provides a step-by-step guide to identify the problematic payout, unsync it within Webgility Desktop, and then refresh and repost the correct data. The goal is to ensure that payout records in QuickBooks Desktop accurately match those in Shopify, supporting clean and consistent financial reporting.

Overview

If a Shopify payout appears missing, incorrect, or stuck when syncing to QuickBooks through Webgility Desktop, don’t worry—it’s usually a quick fix. This guide walks you through how to identify the issue, unsync the payout, and repost it correctly.

Why It Happens

  • Sync mismatches or connection hiccups between Shopify and QuickBooks can sometimes cause payout records to post incorrectly or not at all.

  • The most common issues include missing, duplicated, or misaligned payout amounts.

How to Fix It in Webgility Desktop

Step 1: Locate the Problem Payout

  • Open QuickBooks and go to the Banking or Transactions section.

  • Look for the specific Shopify payout you’re troubleshooting.

  • Confirm the issue: Is the payout missing, mismatched, or duplicated compared to your Shopify payout report?

Step 2: Unsync the Affected Payout

  • Open Webgility Desktop.

  • Navigate to the Payouts section under your Shopify integration.

  • Find the payout in question and choose the option to undo sync.

  • This removes the incorrect record from QuickBooks so it can be refreshed.

Step 3: Repost the Payout

  • Still in Webgility Desktop, click Refresh to pull the latest payout data from Shopify.

  • Locate the payout again in the refreshed list.

  • Select the payout and click Post to QuickBooks (or equivalent) to sync it again.

  • Verify that the payout now shows correctly in QuickBooks under the proper account.

Step 4: Double-Check the Results

  • Open the reposted payout in QuickBooks.

  • Compare the amount and transaction breakdown with the Shopify payout report.

  • Everything should now be aligned and accurately posted.

Tips to Prevent Future Payout Sync Issues

  • Make sure you’re using the latest version of Webgility Desktop.

  • Check that your Shopify integration is active and properly connected.

  • Use appropriate date filters when reviewing payout records in QuickBooks.

  • Refresh data regularly to keep everything current.

In Summary

If a Shopify payout doesn't sync correctly to QuickBooks, just unsync it in Webgility Desktop, refresh the data, and repost. This usually resolves the issue quickly and cleanly—no advanced steps required. Regular checks and keeping your connections active will help avoid issues going forward.