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How to Resolve Undeposited Funds Discrepancies Between Webgility Desktop and QuickBooks Desktop

This article helps Webgility Desktop users resolve discrepancies between Undeposited Funds in QuickBooks Desktop and totals displayed in Webgility Desktop analytics reports. It provides guidance on reviewing and correcting payment processor fee settings and product matching configurations to ensure accurate posting and reporting across systems.

Causes of Issues

  • Incorrect payment processor fee mapping in Webgility

  • Inaccurate or incomplete product matching between your sales channel and QuickBooks

  • Failure to reflect transaction fees correctly in QuickBooks, resulting in mismatch

Step-by-Step Instructions

1. Verify Payment Processor Fee Settings

Make sure your fee mappings are configured correctly in Webgility:

  • Navigate to Connections > Accounting/POS/ERP > Sync Settings > Expense and Fees

  • For each payment processor (e.g., PayPal, Stripe):

    • Confirm that the Fee Account is set to the correct Expense Account in QuickBooks

  • Click Save to apply any changes

2. Adjust Product Matching Criteria

Ensure products from your sales channel match those in QuickBooks accurately:

  • Go to SConnections > Accounting/POS/ERP > Sync Settings > Products > Settings.

  • Locate the option labeled “Select product matching criteria for online orders.”

  • Confirm that products are matched using reliable identifiers such as SKU or Name

  • Modify the matching logic if needed and click Save & Continue.

  • Perform a sync to apply updates

3. Test Configuration with a Single Order

Verify the setup using a test transaction:

  • Post a test order from your sales channel via Webgility

  • In QuickBooks, ensure:

    • The full sales amount appears on the payment/receipt

    • The processing fee is recorded as an expense

    • The Undeposited Funds account shows the net deposit

4. Review Analytics and Reconcile

Compare data between Webgility reports and QuickBooks entries:

  • Confirm Undeposited Funds and posted fees match actual deposits

  • Make adjustments as needed to achieve consistency

Notes

  • Always document changes made to payment mappings and product match settings for future reference

  • Encourage periodic review of these configurations, especially after catalog or integration updates