How Stripe Deposits Work with QuickBooks Online

This article will go over the basics of how Stripe deposits work with QuickBooks Online. 


This feature has two key advantages:

  • It is 100% representative of Stripe settlement activity.
  • Stripe Fees are now subtracted from the settlement rather than the transactions.

What Commerce Sync does is enter all Stripe transactions from a given day as a summary invoice and individually apply each charge as a payment to the invoice:

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All of the payments are initially tracked in a Clearing Account, which is used to track payments that have been authorized, but before they are actually transferred between banks*Note: the clearing account must be set to Undeposited Funds.


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You'll notice in the images above that the $20.00 payment had partial refund for $5.00. Any Refunds are entered as a Refund Receipt and display as a negative entry in Undeposited Funds:

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*Note: The refunds will also reflect any Stripe fees that are also refunded.


Usually on the next business day Stripe will take all Charges and Refunds, collect the Stripe fees from the charges, and then send the final total to your bank account. Commerce Sync represents this activity in QuickBooks Online by entering a Deposit as follows:

  • Each previously entered Payment and Refund Receipt is targeted for Deposit.
  • Stripe Fees are subtracted from the deposit total, rather than the transactions invoice.
  • The net deposit total is transferred into the Bank Account of your choosing.

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