Syncing Shopify transaction fees with QuickBooks Online

A helpful guide on syncing Shopify transaction fees into QuickBooks Online with orders

Written by the MyWorks Team

Updated at May 6th, 2025

MyWorks has the ability to sync your Shopify Payment transaction fees into QuickBooks, making it easy to correctly record these expenses, and reconcile/match your sales with the deposit Shopify sends to your bank.  These can be synced to QuickBooks in one of two ways:

  • Within a Payout that MyWorks syncs to QuickBooks for each Shopify payout
  • As a negative line item inside each QuickBooks order
     

Syncing fees within a Payout 

This is the more common approach, as this helps correctly record the Shopify transaction fees in QuickBooks for each Payout sent to you by Shopify; without having each QuickBooks order containing a negative line item. 

To enable this, simply visit MyWorks Sync > Settings > Payment Methods, and enable the Payout Syncing setting - then select the QuickBooks Expense account to record these fees to. You can learn more about our Payout Syncing feature here.

When Payout syncing is enabled, MyWorks will sync a journal entry to QuickBooks each time a Shopify payout is sent to your bank. This will correctly record the deposit amount in QuickBooks as well as the transaction fees associated with the payout.  

     

Syncing fees as a negative line item

Visit MyWorks Sync >Settings > Payment Methods, and enable the setting to sync transaction fees as a negative line item. In the dropdown option below this setting, choose the product in your QuickBooks that should be used as this negative line item in each order. 

Don't have a product in QuickBooks for this yet? See below for a helpful example to easily create one. Tip: if you've just created this product in QuickBooks, you may have to refresh products in MyWorks Sync > Map > Products. 

 

Then, in orders synced to QuickBooks, the transaction fee will be present as a line item, and the order/payment total in QuickBooks would be the “net” amount you receive from the Shopify order.

 

Creating an item in QuickBooks

Don't yet have an item in QuickBooks to use for this transaction fee line item? No problem, it's easy to create one yourself! Here's the steps, and a helpful video that show how to easily create this in QuickBooks.

  1. In QuickBooks, visit your Products & Services - and create a new product. You can name this anything you'd like, but normally it would be named Transaction Fee or Shopify Fees. 
     
  2. In the “Income Account” section of the product, select the expense account in your QuickBooks Chart of Accounts that these fees should be recorded to. This may be an account already in your QuickBooks Chart of Accounts, otherwise you can create your own! This account is normally named something like Bank Fees, Transaction Fees, or Credit Card/Merchant Fees.  

See the below video to see these steps in action!