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Buy now & saveThanks for joining this thread, @DebGer. I'm here to help you fix and match your old transactions without any further delay!
You have two options on how to handle merchant fees. You can use the Resolve Difference option to fix your payment difference. This helps match your transaction through its difference until it will be equal to zero.
As another option, you can create a bank deposit for the merchant fee less than the amount of the invoice or sales receipt. This way, you can match this transaction to the downloaded bank transaction. You'll have to enter the merchant fee as a line item in the "Adds fund to this deposit" section. Then, select your new merchant fee expense account and enter a negative value that reflects the bank fee amount. For more detailed instruction, go to the What about recording Bank Fees? section in this article: Bank Deposits.
Once done, you can reconcile your account to make sure your books are accurate. Just go to the Accounting menu from the left pane and select Reconcile.
For more insights about this process, please refer to these articles:
Drop me a comment below if you have any other questions. I'll be happy to help you further. Have a great day.