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Hi there, @ago.

You'll want to make sure that the payment is selected in the Select the payments included in this deposit section so you can add the fee as a negative amount. Let me guide you through the steps.

1. On your Bank Deposit page, choose the payment you want to deposit in the Select the payments included in this deposit section.
2. In the Add funds to this deposit section, select the expense account for the fees in the Account drop-down.
3. Enter the negative amount in the Amount field, then click Save and close.

Once done, it'll now decrease the total amount deposited.

As always, feel free to visit our QuickBooks Community help website if you need tips and related articles in the future.

Please touch base with me here for all of your QuickBooks needs, I'm always happy to help. Have a great day.