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I appreciate you for performing the steps provided by my colleagues. When receiving less than the due amount on the invoice because of Bank/Square fees, you'll first need to create an expense account for Bank Fees (if you don't have one already). Then resolve the difference when matching the transaction from the Banking page. Here's how to create an expense account:
Once you have an expense account for bank fees, you can resolve the difference between the invoice and the payment when matching transactions. Let me show you how:
Your transaction is now matched off against the invoice and the bank fees are accounted for. Feel free to visit our Banking page for more insights about managing your bank transactions.
I'd like to know how you get on after trying the steps, as I want to ensure this is resolved for you. Just reply to this post and I'll get back to you. Take care always.