Hi there, @mariniaellett.
You'll want to open the deposited and add a bank fee in the Add funds to this deposit section. Here's how.
In your QuickBooks Online (QBO) account:
- Go to the magnifying glass icon and search for the deposit.
- Open the deposit.
- Add a line item in Add funds to this deposit section.
- Select Bank Charges & Fees under the ACCOUNT column.
- Enter a negative amount in the AMOUNT column.
- Once done, click Save and close.

You can also consult your accountant if you want more tips on how to better record this.
Then, in case you need to record a credit card payment, you can check this article for the detailed steps: Record credit card payments
You can always get back to us whenever you have other concerns in the future. Have a great day!