Bank Register Customers Invoice Receive Payment

How do you apply customer payment that has a merchant fee to an invoice in QBO?

You will need to group both your deposit and fee together so your deposit in QBO matches the bank deposit that was made in real life.

Here’s how to handle it in QBO at this time:


  1. Create an Invoice for your customer as you normally would.
  2. From the home page screen, click the Create icon (+) when you’re ready to receive the payment from your customer.
  3. Choose “Receive Payment” from the dropdown that appears.
  4. Fill out the Receive Payment as you normally would, but ensure the Deposit to field reads “Undeposited Funds” account.
  5. Click Save and close.
receive payment deposit to uf
receive payment deposit to uf



  1. From the home page screen, click the Create icon (+) when you’re ready to get the deposit, minus the fee, in your bank account.
  2. Choose Bank Deposit (under Other) from the drop-down that appears.
  3. Check off the payment from this customer (and any other payments in the batch).
  4. In the Add New Deposits area, enter in the fee as a negative number, so it reduces the overall deposit total.
  5. Click Save and close.
payment minus fee
payment minus fee

This will then match the deposit made to your bank account and record the proper account.



Apps Banking Transactions Tutorial Videos

QuickBooks Online: How to Record Fees from Credit Cards, PayPal, Merchant Services

Your customer paid the Invoice in full amount, but then fees are taken out by your credit card merchant processor before it is posted to your bank account.
This quick video shows how do you enter it in QuickBooks Online?

QuickBooks Online: How to record fees from credit cards, paypal, square, merchant processors