Square charges fees to process payments. The fees vary as follows based on whether your customer pays you online, in person or via electronic invoice: 2.6% plus 10 cents for in-person transactions (2.5% plus 10 cents with Retail Plus plan). 2.9% plus 30 cents for online transactions or invoices without a card on file (2.6%... Tina Orem writes for NerdWallet.