Can someone tell me how I can adjust a check payment deposits that was received short due to a fee on quickbooks online?

Hi there, @roseochoa44.

I can share the details about managing invoice payments with a fee in QuickBooks Online (QBO).

You can create a deposit to show the invoice payment and the fee deduction. Then, change the status of the invoice to paid by matching it to the deposit. Please refer to the steps below on how to do it.

To create a deposit:

1. In QBO, go to the + New option at the top left, then Bank Deposit.
2. In the Receive From column, select the customer's name.
3. Pick Accounts Receivable in the Account column and enter the amount of the invoice. 
4. From the second line, choose the customer's name in the Received From column.
5. Enter Fee expense in the Account column, then enter the amount in negative. 
6. Click Save and Close.

Once done, here's how to match the deposit to the invoice:

1. Go back to the + New option, then Receive Payment.
2. In the Choose a customer field, pick the name of the customer. 
3. Put check marks in the Invoice and the Deposit.
4. Click Save and Close

To learn more about managing customer payments and deposits in QBO, consider checking out these articles:

• Record invoice payments in QuickBooks Online.
• Record and make bank deposits in QuickBooks Online.

I also recommend visiting our website for more tips and other resources you can use in the future: Self-help articles.

Click the Reply button below if you have more questions about receiving/depositing payments or anything else QBO. I'll be around to help. Stay safe and have a good one.