Average Credit Card Processing Fees. So, what do businesses pay for credit card transactions? If you’re looking for quick numbers, here you go: the average credit card processing cost for a retail business where cards are swiped is roughly 1.95% – 2% for Visa, Mastercard, and Discover transactions. The company that processes your credit card fee, including QuickBooks, as well as Square, Stripe, WePay, and others, take a fee to collect for the credit card companies.These fees are charged every time you do a transaction. At QuickBooks, we charge 2.9% for invoiced cards, plus $0.25 per transaction. Average credit card processing fees range from 1.5% to 2.9% for swiped credit cards. Keyed-in transactions have a higher average processing fee of 3.5% to account for the higher risk. Read on to learn what business owners should know about credit card processing fees, including some smart tips to reduce them.