Let me show you some options to charge your customers for the credit card processing fee in QuickBooks Online (QBO).
As stated by Fiat Lux Asia above, QuickBooks Payments doesn't have this feature. As a workaround, you'll want to create a service item for the fees and manually add it to your invoice. Follow these steps to proceed:
- Go to the Gear icon, then choose Products and Services.
- Click on New, then select Service.
- Enter the name of your service item. (Example: Processing Fee).
- Select the account you'd use to track the processing fees.
- Once done, click Save and Close.
Once completed, add the processing fee as an additional item to your invoice to charge your customers.

Another option is to add negative amounts for the fee together with your transactions when generating the deposit. Here's how:
- From the Bank Deposit window, scroll down to the Add funds to this deposit section.
- Enter the fee as a line item.
- Choose from whom the fee was received in the Received From section.
- Select Bank Charges from the Account ▼ dropdown.
- Enter the amount fee as a negative number. For example, if the fee was US $5, enter –5.
- Review the deposit total with the bank fee. Once everything's good, click Save and close.

On the other hand, here's a resource that you can follow when your customer has overpaid you: Handle a customer credit or overpayment in QuickBooks Online. You can use the credit toward an invoice, refund the customer, or enter the overpayment as a tip in QuickBooks.
Feel free to post again if you have other QuickBooks concerns. The Community forum is always open to answer your questions. Have a great day!
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