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Fix PayPal Fees Missing on WooCommerce Orders in Webgility Desktop

Learn why PayPal transaction fees are missing on initial WooCommerce order downloads in Webgility Desktop and how adjusting your order status settings resolves the issue.

Overview

If you connect WooCommerce to Webgility Desktop and PayPal is your payment processor, you may notice that some orders download without their PayPal transaction fees. The fees appear only after you re-download the same order later. This is a timing issue between WooCommerce and PayPal, and you can prevent it by changing which WooCommerce order status Webgility downloads.

When This Applies

Use these steps when PayPal fees are missing on newly downloaded WooCommerce orders in Webgility Desktop, when the fee shows up only after a manual re-download, and when the Download Settings on the sales channel currently include Processing order status.

Why This Happens

WooCommerce marks an order as Processing as soon as PayPal captures the payment. PayPal's transaction reporting, including fee details, can take up to three hours after that capture to become available. If Webgility downloads the order during that window, the fee details are not yet published by PayPal, so Webgility stores the order with no fee. When the order later moves to Completed in WooCommerce and you re-download it, PayPal has had time to publish the fee and Webgility picks it up.

Steps to Change the Download Status

Step 1: In Webgility Desktop, use the sales channel selector in the top-right corner to switch to your WooCommerce store.

Step 2: Go to Connections > Sales Channels > Settings and open the Download Settings section.

Step 3: Uncheck Processing and leave Completed selected, then save the settings. For the broader order-download walkthrough, see How to Download Orders in Webgility Desktop. To re-download the already-downloaded orders that are missing fees, follow How To Download Orders From a Backdate.

Step 4: Trigger a fresh download. New orders are now pulled only after they are marked Completed in WooCommerce, so their PayPal fees should be present on the first download.

Important Note

Note: Changing the download status to Completed only also delays when orders reach QuickBooks. If you need orders in QuickBooks sooner than they are marked Completed in WooCommerce, keep Processing enabled and plan to re-download the few orders that come through without their fees instead.

Key Recommendation

For PayPal-heavy stores, the Completed-only setting usually trades a short posting delay for clean first-time fee data, which saves manual QuickBooks adjustments later.

Additional Support

If PayPal fees are still missing on orders downloaded after they moved to Completed, contact Webgility Support with the WooCommerce order numbers, the download timestamps, and a sample Webgility log from the day the orders were pulled.