Are you B2B or B2C? You should consider having a 3rd party payment processor to integrate with QBO.

I'm happy to assist you with your merchant fee, @change my password. Let me share more information.

We are unable to add this automatically to your customer payment. However, we can create a service item and manually add it to the invoice. You can also consider a third party to integrate with QuickBooks. You can follow these steps to add the service item:

1. On the left panel, click the Get paid and pay.
2. Choose the Products and Services.
3. Select New, and click Service.
4. Enter the name of the service item. ( Example: Merchant Fee)
5. Choose the account you want to track the fee.
6. Hit Save and Close.

Once done, we'll add the credit card fee as an additional item on the invoice to charge the processing fee to your customers. Here's how:

1. On the Invoice page, click Add line.
2. From the Products or Service dropdown, choose the processing fee you've created.
3. Hit Save and Close.

You can also visit the QuickBooks Apps Center if you'd like to use a third-party app.

Moreover, let me share this article that you can refer to if you want to know when QB deposits the payments: Find out when QuickBooks Payments deposits customer payments.

Don't hesitate to reply on this thread if you still have questions about your processing fee. Have a great day ahead, and take care.