Shopify card-processing fees pay for processing a payment. Shopify third-party transaction fees are a separate platform charge that can apply to certain payment routes. Your subscription is another cost again. There is no single percentage that describes every merchant, payment method, country, and order.
Start with the provider used on the actual transaction, then check the applicable fee schedule. Activating Shopify Payments does not make all other gateways free of additional Shopify charges.
Which fee are you looking at?
| Charge | What to inspect | How to put it in a budget |
|---|---|---|
| Card or provider processing | Payment provider and applicable rate | Percentage and fixed amount per transaction |
| Shopify third-party transaction fee | Eligible payment route and plan | Separate percentage on the applicable amount |
| Subscription | Plan and billing interval | Fixed operating cost |
| Currency-related charges | Currency and conversion path | Separate line when applicable |
| App or service fees | Subscription, usage, or per-order agreement | Classify using the actual billing terms |
Shopify's third-party provider documentation explains the additional charge and exceptions. The billing guide for third-party transaction fees explains the calculation and special payment cases. Check current rates for your country and plan in your account and the pricing page.
What does a $100 order cost?
These are illustrative rates, not a current Shopify plan quote. Assume the fee base is $100, card processing is 2.9% plus $0.30, and an additional platform fee of 2% applies only in the third-party scenario.
| Scenario | Calculation | Total modeled payment fees |
|---|---|---|
| Processing only | $100 × 2.9% + $0.30 | $3.20 |
| Processing plus additional fee | $3.20 + $100 × 2% | $5.20 |
The processing-only case leaves $96.80 before product cost, shipping, subscriptions, refunds, and tax. That amount is not profit. The second case leaves $94.80 before those other costs.
On a $15 payment, the same 2.9% plus $0.30 processing formula rounds to $0.74, approximately 4.93% of the amount collected. The fixed charge matters more on small orders. You cannot estimate total processing expense accurately from a percentage alone when average order value is low.
Check the exceptions by payment route
For payments processed through Shopify Payments, distinguish its processing charges from additional third-party fees. If an order instead uses another gateway, activating Shopify Payments elsewhere in the store does not automatically remove the additional fee on that gateway.
Shopify documents a PayPal exception when Shopify Payments is activated. PayPal's own processing costs remain a separate question, and the PayPal product available differs by location. Our Shopify Payments, Stripe, and PayPal comparison explains why the provider label needs more context.
Shopify's manual payment documentation states that manual payments do not incur its third-party transaction fee. Bank transfers and cash on delivery still have operational and possible third-party costs; use the manual payment workflow to assess them.
For the product and redemption workflow, use the Shopify gift-card setup checklist.
Gift-card and store-credit redemptions need separate attention. The current transaction-fee billing guide describes additional fees on those tendered amounts for stores created on or after May 12, 2025, with a documented Plus exception. Inspect those transactions rather than assuming every order containing a gift card has the same treatment as a normal card-only sale.
Include shipping, discounts, and refunds correctly
Shopify's documented third-party fee base includes product value after discounts, plus applicable tax and shipping. Your payment provider has its own processing terms. Calculate each fee using its relevant base instead of blindly applying both percentages to the product's list price.
For Shopify Payments refunds, the original card-processing fee is not reimbursed. Other provider and transaction-fee refund treatment should be checked against the applicable account and regional documentation. Avoid a model that automatically assumes every fee reverses when revenue is refunded.
The 100-order returns budget shows how an unrecovered fee affects contribution and cash requirements.
When should you upgrade to reduce fees?
Divide the extra subscription cost by the effective percentage saving on eligible volume, then include any fixed-fee differences. Do not apply a card-rate saving to sales that use a different payment method.
For example, a hypothetical $60 monthly upgrade that reduces an applicable rate by 0.2 percentage points needs $60 ÷ 0.002 = $30,000 in eligible monthly volume to break even on that rate alone. Features may justify a different decision. Use the plan-upgrade worksheet for the complete comparison.
Before launch, record your plan, country, provider mix, average order value, and expected refunds. Put those inputs in the startup calculator, then reconcile the estimate with the first real bill and payout.