IS there a way to automatically charge the customer the 2.99% fee if they pay with a credit card?

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

I acknowledge that having the functionality to automatically charge your customers when they pay with a credit card is essential for your business needs, Ryan.

Although QuickBooks Online doesn't have a built-in feature for automatic charging, you can create a service item and manually add it to your invoices.

To create a service item for the fee, you can follow these steps:

1. Go to the Sales menu. Click Products & services.
2. Pick New, then choose Service.
3. In the Name field, enter the name of the service. (Ex. Credit Card Fee)
4. Select the account you'd use to track the processing fees.
5. After completing all details, Save and Close.

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

1. Click + New, then Invoice.
2. From the Product or Service dropdown, pick the service fee you created.
3. You can add a note about the fee in the Note to Customer section.
4. Once done, Review and send.

Here is an article you can refer to for the detailed steps: Manually add service fees to invoices in QuickBooks Online.

You may also want to consider integrating a third-party app with your QuickBooks, as suggested by 4Gal, for the automatic charging of fees.

Feel free to explore our third-party apps by following these steps:

1. Hover over the Apps menu from the left panel.
2. Click the Find Apps tab, then type in the keyword. 
3. Once done, you can choose from the lists that suit your business needs. 

Moreover, you can set up invoice reminders automatically in QuickBooks. This feature helps you save time while informing customers of their payment due dates.

Following the workaround and exploring our third-party website, you can automatically apply fees when your clients pay using credit cards. Please feel free to reach out if you have any further questions. Have a great day!