The short answer
Your store plan, your payment provider, and Shopify's third-party payment fee are separate costs. Which ones apply depends on who handles each payment. Do not add every rate on the pricing page to one sale. Start with one order and find its payment provider, amount, and fee.
In this guide
Give each cost a name
The plan fee pays for your Shopify plan. A processing fee pays the company that handles a payment. A third-party transaction fee is a separate Shopify charge that can apply when another company takes payment.
A merchant asked whether all the listed card rates add up. They do not. Read the rate for the provider used on that order.
See Shopify's payment fee guide for the two setups.
- 01Plan
A fixed subscription cost.
- 02Processor
A fee to handle that payment.
- 03Shopify extra fee
Applies only to fee-eligible payment amounts.
When Shopify Payments handles the card
Use the Shopify Payments rate for that payment. Do not add the general third-party fee just because it appears on the plan page.
The card type, market, and setup can change the rate. Some stores use a direct card provider alongside Shopify Payments. That specific setup adds a 1.25% premium to payments handled by Shopify Payments.
That is a reason to copy your actual rate. It is not a reason to add 1.25% to every store's card payments.
When another provider handles the card
A made-up example: the provider charges 3% plus 30 cents. The applicable Shopify third-party fee is 2%. On a $100 fee-bearing payment, that is $3.30 plus $2: $5.30 in those fees.
Do not add a Shopify Payments card rate on top of that same third-party payment.
Shopify's third-party fee base includes the item amount after discounts, plus tax and shipping. Use the right amount, not just the item's shelf price.
What about PayPal, cash, and gift cards?
With Shopify Payments active, PayPal Express Checkout is exempt from Shopify's third-party fee. PayPal's own processing fees can still apply. Other gateways do not all get this exception. See Shopify's provider rules.
Manual payments and POS orders have exceptions too. For stores created on or after May 12, 2025, gift-card and store-credit amounts have special third-party fee rules.
Check the current rule for your payment method. An old forum answer may no longer fit. If your store has a Plus contract, check its terms separately.
Follow one real order
Pick an order you understand. Write down the date, provider, amount, and fee. Check Shopify's bill as well as the provider's record.
For Shopify Payments, payout details and exports help you find the amount, fee, and net payment. Match dates when you compare records.
Keep refunds, currency costs, and disputes separate. They can make a payout differ from a simple sales estimate.
Then see whether a higher plan helps
Enter the same payment amounts for both plans in the plan upgrade calculator. Add the plan fee, the relevant percentage fees, and fixed fees per payment.
The result covers the costs you enter. It is not your full store bill. Keep app charges and other costs in your shop budget.
Read Basic vs Grow before you switch. A lower card rate helps only when the savings and useful features are worth the extra plan cost.
Sources & notes
Sources checked 2026-09-14. Product facts come from the links below; examples explain the steps. Read our research method and testing limits.
- Shopify Payments fees help.shopify.com
- Shopify third-party provider rules help.shopify.com
- Shopify third-party fee calculation and exceptions help.shopify.com
- Shopify Payments alongside a direct provider help.shopify.com
- Shopify payout details help.shopify.com
- Merchant question: which payment fees add up? community.shopify.com