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:

RECEIVE PAYMENT

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.

BANK DEPOSIT

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.

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

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