We're unable to automatically charge convenience fees for credit card payments in QuickBooks Online. You'll need to do it manually by adding a new line item on your customer's invoice for the convenience fee.
On your invoice transaction, click an empty line below the Product/Service column.
Select Add new from the product or service drop-down.
Enter the description of the convenience fee on the Name field.
Click Save and close.
Once done, enter the Rate.
Click Save and Close.
You can also record credit card charges directly from the Merchant Services Center. Please check out the Process a Credit Card payment section of this article to know more about the process: Process a Payment in Merchant Service Center.
Having the option to automatically set convenience fees for client's, who prefer to use debit/credit cards as their payment method, is time efficient. I'll personally forward this request to our developers who rolls out product enhancements and updates.
If you have other questions or clarifications about this topic, let me know in the comment. I'll be more than happy to provide further assistance and insights about payments processing in QuickBooks. I got your back. Take care!