Handling Transaction Fees with PayPal

If you have PayPal enabled as a gateway in WooCommerce, you’ll have the option in our Map > Payment Methods > Advanced Options 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 fee syncing for PayPal fees in our sync, 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.

As you can see in the screenshot above, you will see two transactions in your Banking tab for each PayPal sale:

  1. The actual gross amount of the sale ($6.99 above). This will be matched to the invoice or sales receipt we already have synced into QuickBooks.
  2. The PayPal transaction fee ($.48 above). This will always contain the description “NAME Fee Amount”. You can either add it manually by clicking Add, or create a bank rule, like shown above, that automatically adds transactions containing the description “Fee Amount”.

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 sync 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.

You can read more about connecting your PayPal account correctly to QuickBooks Online here. 

Updated on December 30, 2019

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