Shopify Plus Depending on your package, Shopify has a per-transaction fee. For online credit card transactions, Shopify has a rate of 1.6%-2.2% plus a flat rate of 20p per transaction. For in-person credit card transactions, Shopify has a rate of 1.5-1.7%. For payments processed by other providers (non-Shopify payments), Shopify has a rate of 0.5-2%.