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Troubleshooting Missing PayPal Transactions in QuickBooks Desktop via Webgility Desktop

This article helps Webgility Desktop users identify and resolve missing transaction issues in QuickBooks Desktop that often result from incorrect fee or expense settings, particularly when using third-party payment processors like PayPal. It explains how misconfigured fee mappings can cause PayPal transactions to fail syncing and provides steps to correct these errors.

Root Cause: PayPal Fee Not Mapped in Webgility's Expenses & Fees

When PayPal transaction fees are not properly mapped within Webgility’s Expenses & Fees settings, posting failures may occur. As a result, PayPal transactions may not sync to QuickBooks, leading to inaccurate financial records.

 

Steps to Set Up Fees in Webgility

  1. Go to Connections > Accounting/POS/ERP > Sync Settings.

  2. In the configuration menu:

    • Navigate to Expenses & Fees.

    • Check the box: “I want to record payment fees.”

  3. You’ll now see the option to select a line item for Paypal Fee.

  4. If the payment fee item doesn’t exist in QuickBooks:

    • Create a Non-Inventory Part item.

    • Assign it to a Payment Processor Fees account (or similar).

  5. In Webgility:

    • Click the refresh icon in the lower-right corner of the configuration window.

    • Under Record Payment Fee As, select the relevant QuickBooks line item.

    • Click Save & Close.

Note: The option “Refund recorded payment fees” is not required if using a line item setup for fees.

PayPal Fee Connection & Setup

To record PayPal fees as a line item, follow these steps:

  1. Integrate PayPal with Webgility:

    • Click the Gear icon for the fee connection.

  2. On the setup page:

    • Enter your PayPal API credentials (Username, Password, Signature).

    • Click Save.

This does not require your PayPal email or password.

  1. Once connected:

    • Select Line item as the method to record PayPal Payment Fees.

    • Choose your existing QuickBooks line item for PayPal Fees.

    • Click Save.