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Resolving Shopify Payout and Gift Card Reconciliation Issues in QuickBooks Using Webgility Desktop

This article helps users of Webgility Desktop troubleshoot and resolve common reconciliation issues between Shopify payouts and QuickBooks Desktop, especially when handling gift card payments, refunds, and clearing account balances. It walks users through reviewing transactions, verifying mappings, and using Webgility tools to manually resync or correct payout records. The goal is to maintain accurate accounting and prevent syncing errors.

Overview

If you're noticing mismatches between your Shopify payouts and QuickBooks entries—such as negative clearing account balances, incorrect handling of gift card transactions, or payout posting failures—this guide is here to help. These common issues can be easily addressed by reviewing your Webgility Desktop settings and taking a few corrective steps.

Common Issues You May Notice

  • Negative balance in your Shopify clearing account in QuickBooks

  • Invoices showing unpaid due to gift card-related errors

  • Shopify payouts not posting properly to QuickBooks

  • Refunds or gift card payments not linking correctly to orders

Steps to Resolve

1. Review Shopify Payout and Order Data

  • Go to Shopify Admin > Settings > Payments > Payouts

  • Export the latest payout and order reports

  • Check for any mismatches in amounts, dates, or payment methods

2. Check Your QuickBooks Clearing Account

  • Open QuickBooks > Chart of Accounts

  • Locate the Shopify Clearing Account

  • Look for negative balances or incorrect entries related to payouts

3. Verify Gift Card Transactions

  • Identify orders paid with gift cards (partially or fully)

  • In QuickBooks, ensure gift card payments are mapped to the correct accounts

  • Check for duplicated income or missing entries related to gift card sales

4. Fix Refund and Payment Linkage

  • In Shopify, double-check completed and voided refund records

  • In QuickBooks, match each refund with the correct payout or order

  • Update links manually if necessary to ensure everything aligns

5. Re-Sync and Repost Affected Payouts

  • Use Webgility Desktop to manually sync Shopify and QuickBooks

  • If any payouts failed, delete those entries in QuickBooks and re-import them

  • Review how refunds and gift cards are being handled in your Webgility settings

6. Handle Unresolved Transactions Manually

  • For unmatched orders or payments, mark invoices as paid/unpaid manually based on Shopify data

  • If needed, use journal entries in QuickBooks to adjust balances correctly (e.g., for liabilities or write-offs)

Tips for Ongoing Accuracy

  • Perform regular reviews of your Shopify and QuickBooks integration

  • Reconcile payouts and refunds at least once a week

By following these steps in Webgility Desktop, you can quickly restore accurate reconciliation between Shopify and QuickBooks—keeping your books clean and your operations smooth.