Welcome to the Community, Killian.
I'd be glad to provide information about matching the transaction to an invoice in QuickBooks Online (QBO).
Based on what you've said, it seems that your fees have already been brought or recorded into QBO, and you're wondering how to automatically reconcile the difference when trying to match the invoice with the bank transactions. However, it's not possible to automatically match the discrepancy between the fees on the invoices from the matched bank transactions to the fees that are already recorded in QBO.
I recommend not matching your bank transactions to the invoice as it may cause a conflict in QBO. Instead, I suggest excluding your bank transaction and manually marking the invoice as paid by recording a received payment for you to properly reconcile it.
Moreover, I also recommend reaching out to your accountant to further assess the actual situation and explore possible alternative solutions for the bank transactions and the invoice and to see if there are other ways to work around it.
I'll also add these articles to help you review your beginning balances and fix issues for accounts you've reconciled in the past:
In case you have any follow-up questions about matching the transaction or anything else related to QuickBooks, feel free to ask me. I'm always here to help you, Killian. Take care!
