Syncing Shopify Payouts to QuickBooks Online with MyWorks

Discover how to effortlessly sync your Shopify payouts with QuickBooks Online using MyWorks for seamless reconciling.

Written by the MyWorks Team

Updated at May 6th, 2025

In addition to syncing individual orders from Shopify to QuickBooks Online (as Sales Receipts or Invoices/Payments) - MyWorks also includes the ability to sync a Shopify Payout into QuickBooks, making it even easier to reconcile deposits received in your bank account from your Shopify sales with the individual orders MyWorks creates in QuickBooks. 

Overview

Since MyWorks already syncs individual orders from Shopify into QuickBooks; the sale/payment is already correctly recorded in QuickBooks. By syncing a Shopify Payout into QuickBooks in addition to these orders; this helps more easily reconcile these individual orders in QuickBooks with the single deposit sent to your bank account by Shopify several days later.  

When Payout Syncing is enabled in MyWorks, a Journal Entry will be created in QuickBooks each time a Payout is created/sent to your bank account by Shopify. This will correctly record the amount of the payout to your QuickBooks Bank account, removing the funds from your clearing account in QuickBooks and correctly recording the transaction fees: making it simple to “match” once the Shopify Payout reaches your bank account in real life. 

MyWorks supports syncing Payouts for all orders paid through Shopify Payments.

 

Steps to enable

Visit MyWorks Sync > Settings > Payment Methods, and enable the option for Payout Syncing. 

  1. Set a QuickBooks Bank account to record the payout to - which should be your Checking account where these deposits are received in real life.
  2. Set a Transaction Fee Expense account - which is where the Shopify transaction fees will be recorded.
  3. Ensure the first “QuickBooks Online Bank Account” is set to a “clearing account” bank account in QuickBooks like a bank named “Shopify Clearing Account”. 

Syncing new payouts automatically

Once the above Payout syncing is enabled in MyWorks Sync > Settings > Payment Methods; payouts can sync to QuickBooks in two ways - automatically, and manually. 

To automatically sync new Payouts as they're sent to your bank from Shopify; visit MyWorks Sync > Settings > Automatic Sync, and enable the Payout option. Then, when a new payout is sent to your bank from Shopify, MyWorks will automatically record this in QuickBooks for you.    

Pushing payouts manually

It's also possible to push payouts manually to QuickBooks - which can be helpful if you're syncing past orders into QuickBooks to “catch up”.  

This can be easily done by visiting MyWorks Sync > Push > Payouts, where you'll see a list of past Shopify Payouts and can easily select and push these to QuickBooks.

 

Example

Below is an example of a Payout sent from Shopify for three sales on April 7th. MyWorks synced all three sales to QuickBooks, recorded to the Shopify Clearing account - and the Payout helped correctly record the funds being deposited to the Checking account in QuickBooks, less the transaction fees.

Before the payout syncs to QuickBooks:

 

After the payout synced to QuickBooks: 

 

Tips

  • Payouts will only sync to QuickBooks for orders paid by Shopify Payments, not any 3rd party payment methods like PayPal or Authorize.net. 
  • As soon as the Shopify Payout is created by Shopify, it would show in the Finance > Payouts area of your Shopify store - and would be synced to QuickBooks by MyWorks shortly after that. 
  • Payout syncing includes support for changed orders and refunds, as each Shopify Payout would be accurately re-created in QuickBooks, including any charges, refunds, or fees that are part of that Payout.