If you have PayPal enabled as a gateway in WooCommerce, you’ll have the option in our Map > Payment Methods to enable transaction fee syncing, where we sync the transaction fee for the payment over to QuickBooks Online as a separate journal entry. You can read more about this in our Transaction Fee Syncing article.
However, we recommend you NOT enable transaction syncing for PayPal, as if you connect your PayPal account to your QuickBooks Online bank account in QuickBooks Online – as you should – then transaction fees will be automatically pulled in from PayPal as a transaction in your Banking tab in QuickBooks. From this Banking tab, you can easily add the transaction to QuickBooks, and/or add a Banking Rule to automatically recognize/add the transaction to QuickBooks.
This method is recommended, as it’s the most efficient/effective way to ensure all your transaction fees for PayPal are recorded correctly and accurately. If our integration was also syncing transaction fees for PayPal, you’d have to match them on this screen instead of adding them – and aside from being redundant, it opens up the possibility for a transaction fee to be double-recorded in QuickBooks.