The way in which merchant discount fees appear on your bank statement depends on how the fees are deducted by the merchant account processor. Fees are deducted in two ways:
Most merchant account processors accumulate the fees during the statement cycle (usually a month), then deduct them from your bank account at the end of the cycle. Your monthly bank statement shows each deposit and a single fee charged at the end of the month.
Other merchant account processors deduct fees each time a deposit is made. This is usually done when the merchant account processor deposits payments on a daily or weekly basis. In this case, your monthly bank statement shows a fee for each deposit (that is, two separate transactions each time).
The merchant discount fees are not shown on your bank statement. It shows only the net deposit amount, which is the total of all your credit card payments for that day minus the total merchant discount fees charged for that day.
Deposit = total credit card payments - total merchant discount fees
In either case, use the Check page to appropriately account for the fees in QuickBooks.
If you use QuickBooks Payments to process credit cards and online invoice payments, QuickBooks automatically records the fees for you as an Expense. You don't have to use the Check page to record those fees.