Hi Nickie, please make sure that you have allocated the invoice payment to Undeposited funds (steps 1 & 2). The invoice payment should be for the full amount including fees, as these will be deducted at the next step (the bank deposit). Undeposited funds is a default account in QuickBooks Online used for holding customer payments until you receive them in your bank.
Payments allocated to undeposited funds will appear under Select the payments included in this deposit on the bank deposit. After ticking the relevant payment(s), scroll to Add funds to this deposit to deduct the fees.
