If a Customer wants to pay with a credit card can I charge them the credit card processing fee (like 3%) when they make payment? Also, can it be added automatically?

As of now, the processing fee is charged to the owner of the QuickBooks account who availed the Merchant Services, coastlinewastesolutions. We can also create an item for the processing fee, and add it manually to their invoices.

Your customers will only pay the amount mentioned on their invoices. The fees are deducted from those payments before it completely hits your bank account. You can follow the exact steps when processing electronic payments in QuickBooks Online: Receive and process payments in QuickBooks Online with QuickBooks Payments.

Meanwhile, you'll have to manually add the processing fee to the customer's invoices if you want them to pay for. I'll lay out the process on how you can create a processing fee item and add it to the invoices.

1. Create an expense account that tracks processing fees.
   It is not necessary to create one if you already have it in your Chart of Accounts.
2. Click the gear icon in the upper-right corner, and select Products and services.
3. Select the New button, and choose Service.
4. Enter the desired name for the processing fee item.
5. In the Income account field, enter the the expense account you created earlier.
   It is located next to the Sales price/rate field.
6. Click Save and close.

After creating the item, you can already add it to your customer's invoices on top of the item or services they have availed from you.

When you record the payments in QuickBooks Online, make sure you enter the same amount mentioned on the invoices. You can use this link for reference: Record invoice payments in QuickBooks Online.

We will offset the processing fees the moment we create a bank deposit. Make sure you follow the Include bank or processing fees section in this article: Record and make bank deposits in QuickBooks Online.

Let us know if you have clarifications or questions regarding the process of receiving customer payments in QuickBooks Online. We'll be glad to provide you details on this.

@coastlinewastesolutions 

You need to use a 3rd party payment processor to do so.