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Fixing PayPal Payments Posting to Wrong Account in QuickBooks Desktop via Webgility Desktop

This article helps Webgility Desktop users resolve issues where PayPal payments are posting to the wrong account in their QuickBooks Desktop, such as appearing under Shopify Payments instead of PayPal. This problem is typically caused by incorrect payment method mapping and can affect reconciliation and reporting accuracy.

1. Go to Sync Settings

  • Open Webgility Desktop

  • Navigate to:
    Connections > Accounting POS/ERP > Sync Settings

2. Access Payment Method Mapping

  • In Sync Settings, open the Orders tab

  • Click on Configure Mappings under Map Payment Method

  • Then click Setup

3. Add or Map the Payment Method

  • In the Setup window:

    • If not already listed, add PayPal as a payment method

    • Optionally, set a Default Payment Method for unmatched entries

4. Map Payment Methods to Correct QuickBooks Accounts

  • Use the dropdown menus to map:

    • PayPal → to your PayPal Account in QuickBooks

    • Other methods (e.g., Shopify Payments) → to their correct accounts

5. Save and Apply Changes

  • Click Save and Close

  • Then click Save & Continue in Sync Settings to apply your updates