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Troubleshooting Due Balances, Refunds & Order Total Discrepancies for Shopify orders in Webgility Desktop

This article helps Webgility Desktop users resolve issues related to missing or incorrect due balances, refunds, and order total mismatches when posting Shopify orders to QuickBooks Desktop. It outlines how to investigate discrepancies, explains current integration limitations such as the default behavior of not syncing outstanding balances and provides manual workarounds

Overview

If you’re experiencing issues where due balances, refunds, or order totals aren’t syncing correctly between Shopify, Webgility Desktop, and QuickBooks, this article will help you troubleshoot and understand your options.

Common Issues You Might See

You may notice one or more of the following:

  • Due balances from partially paid Shopify orders aren’t syncing into Webgility or QuickBooks.
  • Refunds aren’t being downloaded or posted correctly.
  • The order total in QuickBooks doesn’t match what you see in Shopify.
  • Your Webgility integration is only syncing the authorized or paid amount, not the full total or outstanding balance.

Step-by-Step Troubleshooting

1. Review the Shopify Order Details

Log in to your Shopify Admin, and check the affected order(s) for:

  • Total amount
  • Amount authorized/paid
  • Outstanding (due) balance
  • Any recorded refunds

This helps you verify whether the issue starts with how Shopify is tracking the payment or refund.

2. Check Webgility Integration Settings

In Webgility Desktop, go to:

Connections > Settings, then review:

  • What order statuses are set to sync (e.g., Paid, Partially Paid).
  • Whether refund downloads are enabled.
  • Note: Webgility does not sync outstanding/due balances by default—only the authorized/paid amounts are posted to QuickBooks.

3. Review Sync Logs in Webgility

Go to C-Drive > Logs

  • Find entries related to the problematic orders.
  • Look for any error messages, skipped records, or notes about missing refund or balance data.
  • Capture timestamps or log details if you need to reach out to support.

4. Compare Orders in QuickBooks

Open QuickBooks and locate the same order:

  • Compare the total amount, any refunded values, and line items.
  • Check if there’s a missing due balance or refund entry that didn’t sync.

Workarounds & Next Steps

Manual Adjustments in QuickBooks

Since due balances aren’t automatically synced, you may need to:

  • Manually add refunds or balance adjustments as line items in QuickBooks.
  • Use memos or custom fields to mark them for tracking purposes.