I'll share some insights about how credit card processing fees work in QuickBooks Online (QBO), @peter124.

Settling up an automatic 3% fee for credit card payments is unavailable in QBO. Instead, you'll have to manually apply the fee to the transaction. To do so, you can create a Non-inventory or Service item, and then manually add it to the invoice. You can also consider a third-party app and integrate it with your QuickBooks. 

Follow these steps to set up a Non-Inventory or Service item for the credit card fee:

1. Click on the Gear icon located on the top right.
2. Select Products and Services.
3. On the Products and Services list page, click ‘New’ in the upper right corner.
4. Choose Service or Non-Inventory.
5. Fill in the necessary information.
6. Click Save and Close.

Once done, add the credit card fee as an additional item on your invoice when you charge your customers with the processing fee.

Also, it's a good idea to tell customers about the charge before you invoice them. You can include the default email message in your sales forms, just click this article for more info: Customize invoices, estimates, and sales receipts in QuickBooks Online

Furthermore, I'm adding these resources that might help you with your future tasks in QuickBooks: 

• Change product and service item types in QuickBooks Online
• Set up and apply automatic late fees to invoices

If there's anything else you need assistance with aside from setting up automatic fees, never hesitate to ask below. The Community team is just a click away. 

@peter124 

Yes there is. Use a 3rd party payment processor to integrate with QB.

This is horrible, and one reason I am looking to move away from QBO and paying $90/month.  As a business owner I do not know when a customer will choose to write a check or pay with a CC. If you have 200 invoices going out how do you email each one? And then handle responses, apply the fee here and there. It is EXTREMELY inconvenient. And not to mention it comes across as petty to a customer who does not handle receiving payments via CC....and how it adds up.  Plus when you add 3% to your invoice it raises the amount you will need to charge to get what you are owed..........SUCH A PITA.

Yes, it’s a real pain. I put the card fee on there and say with bank transfer it’s waived but would be so much easier to be able to automatically process fees for card payments. 

@YV Carpet Cleaning 

If you run a B2B company, you can use a 3rd party processor to integrate with QB and accept payments for free.

Who would you recommend please? I tried couple of them and didn't work for Quickbooks :--((

@Gigacrete 

You are running B2B, correct? You should contact @Fiat Lux - ASIA for details.

Quickbooks sure can automatically charge you the fee though can't they!!! 

@bmayfield76 

You can use a 3rd party payment processor to integrate with QB.

Is there a 3rd party processor that does not charge outrageous fees of their own??  Up for some recommendations ... Does it implement within Quickbooks itself?? I don't want to have to be going all over the internet to run a credit card.  Does it give credit automatically to the invoice itself??