How do most companies deal with payments via credit card not matching up up with the original amount invoiced?

Hi there RTBrew,

I'm happy to hear you're using the connection to your bank in QuickBooks Online. It's a feature that saves you time and makes it easier to categorize your transactions. It's vital that the processing fees on your credit card payments be accounted for in order for your bank balance to be correct. I can provide some insight into this.

As explained by lashedlifter, you can add the fees when you create the deposit of your payment. This article about How to account for Bank Fees when matching transactions in Bank Feed goes into detail on how to add those fees when matching.

If you don't currently have an expense account to keep track of the credit card fees, you can add it by navigating to the Accounting option in the left column, then selecting Chart of Accounts. Click the New button in the top right, then choose Expense as the Account type, and Bank Charges as Detail Type. Pick a name for the account and Save.

I hope this helps you in matching your sales to your invoices already in QuickBooks Online. If you have any questions or need more information, please reach out here.