If your bank statement shows the sale with the merchant fee deducted

In this example, you've invoiced a customer for a $220 sale. Because they paid using AMEX you incur an $11 AMEX merchant fee. Your bank statement then shows the AMEX payment less the merchant fee ($209).

1. Record the payment for the invoice and select the option Group with Undeposited Funds and select the applicable Payment Method.
   
2. Go to Banking > Prepare Bank Deposit and click Deposit Adjustment. The Bank and Deposit Adjustments window appears.
3. In the Fees and Cash Back section, enter the merchant fee in the Amount field and choose your applicable merchant fees account in the Expense Account field. Check with your accounting advisor if you're not sure which account to choose or if you need to create an account.
   
4. Click Record. A new transaction line representing the merchant fee will appear in the Prepare Bank Deposit window.

5. Select the transactions and the fees that make up the total value of the deposit to your bank account, then click Record.
   

After completing these steps, the sale is closed and you've recognised the AMEX merchant fee. The Bank Register window will now show a single transaction representing what was actually received into your bank account ($209).

Clicking the transaction's zoom arrow displays the breakdown of the transaction, consisting of the payment received and the deducted merchant fee:

If your bank statement shows the merchant fee separately

In this example, you've invoiced a customer for a $220 sale. Because they paid using AMEX you incur an $11 AMEX merchant fee. Your bank statement shows the full AMEX payment including the merchant fee, and also shows the merchant fee being deducted as a separate entry.

1. Record the payment against the open invoice.
   
2. Record a Spend Money transaction for the merchant fee. In our example we've allocated the expense to a merchant fees expense account:
   

Check with your accounting advisor if you're not sure which account to choose or if you need to create an account.