Shopify Payments vs Stripe and PayPal: Fees Explained

title: Shopify Payments vs Stripe and PayPal: Fees Explained slug: shopify-payments-vs-stripe-paypal-fees meta_title: Shopify Payments vs Stripe and PayPal: Fees Explained meta_description: Shopify Payments vs Stripe and PayPal: compare processing and transaction fees, the PayPal exception and plan-specific costs for informed merchant decisions. primary_keyword: Shopify Payments vs Stripe secondary_keywords:

Shopify Payments vs Stripe and PayPal: Fees Explained

Shopify Payments vs Stripe and PayPal is a comparison of processing fees and Shopify's separate third-party transaction fees. For an illustrative US Basic-plan card payment at 2.9% plus $0.30, a $100 Shopify Payments transaction costs $3.20. A hypothetical external gateway charging the same rate plus a 2% Shopify fee would cost $5.20, before other adjustments.

These are US examples, not a promise that a particular gateway is available in your country or eligible for your business. Confirm your plan, processor, currency and current rate card before making a decision.

Separate the fee layers

Shopify's pricing overview explains the difference between processing charges and platform transaction fees. In Shopify's published US pricing, Basic's third-party rate is 2%; rates vary by plan and market. Verify the current pricing page.

The PayPal exception

According to Shopify's third-party provider guidance, when Shopify Payments is your primary payment provider, PayPal transactions are exempt from Shopify's third-party transaction fee. PayPal's own processing fees can still apply. Other third-party and alternate gateways may still attract Shopify fees even with Shopify Payments enabled.

Shopify also documents a 1.25% premium on Shopify Payments transactions in certain configurations using a direct third-party provider alongside it. Read the Shopify Payments fee guidance and check whether it applies to your setup rather than assuming every combination behaves the same way.

A practical cost calculation

For each payment method, calculate: transaction value × applicable percentage, plus fixed transaction fees, plus any applicable platform fee. Add the monthly subscription and conversion, international, refund and dispute costs separately. Do not compare just headline percentages.

For 1,000 hypothetical $100 transactions, a difference of two percentage points is $2,000 before any changes in fixed fees or customer behaviour. That illustration assumes the same eligible transaction value on every order; taxes, refunds and gateway exceptions may change your actual bill.

Why the cheapest rate may not win

An alternative method can be valuable if customers trust it, Shopify Payments is unavailable, or your business category needs another provider. Test conversion as well as fees: losing a legitimate sale to save a small percentage can be a poor trade. Stripe availability and direct integration vary by region and setup; do not assume a direct Stripe account can be used on every Shopify store.

For country restrictions and the consequences of delayed payouts, see Shopify Payments availability and payout holds and reserves.

Verify a statement, not just a sales page

Export a recent month of payment and Shopify billing records. Group transactions by gateway, domestic or international card, currency and order value, then reconcile each fee line against the contract. Consider refund behaviour, payout timing and dispute support as well as transaction cost. Repeat the calculation after changing plans or adding a direct gateway: the interaction can be different from a wallet-only setup.

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