With the integrated ACH Universal add-on to QuickBooks, you don’t pay ACH transaction fees for vendor bill payments.  QuickBooks charges transaction processing fees when you accept ACH payments from customers through QuickBooks Payments. Apply to  Intuit Merchant Services within QuickBooks. The IMS per ACH  fee is 1% of the transaction amount (up to $10) for QuickBooks Online. The per transaction ACH fee is $3 for QuickBooks Desktop.