Crediting surcharges if a customer pays cash

If an invoice is created that includes credit card surcharges, and your customer decides to pay you via check or ACH, they may want to be credited for the surcharge.

You can always edit the invoice and remove them.  This will then reduce the invoice total amount by the surcharge resulting in a credit on account for the customer.

As an example, an Invoice was generated for $100, plus a 3% credit card fee, resulting in an invoice total amount of $103.   The customer then paid you via ACH, but paid the entire $103.  If you want to remove the credit card fee, go into the invoice and delete the line with the fee on it.  This will then make the invoice amount $100.  The extra $3 paid will remain on the customer's account and will be applied to their next invoice automatically.

Note that automatically applying credits is the default setting in QuickBooks, however, if you have turned that setting off you will need to apply the credit manually after the next invoice is issued.  You can check the setting of this by going to QuickBooks Company Settings (click the gear at the top right), then select Advanced and you'll see "Automatically apply credits" in the Automation section.