Shopify Payments is built on top of Stripe's payment infrastructure. This is publicly acknowledged. Both products process cards through the same underlying network with comparable authorisation rates and payment methods supported.
This means the "vs." comparison between Shopify Payments and Stripe is less about underlying infrastructure and more about pricing structure, platform integration, and use case fit.
This is the most important calculation for Shopify merchants:
| Shopify Plan | Card rate (Shopify Payments) | Transaction fee if NOT using Shopify Payments |
|---|---|---|
| Basic ($39/month) | 2.9% + $0.30 | 2% additional fee |
| Shopify ($105/month) | 2.6% + $0.30 | 1% additional fee |
| Advanced ($399/month) | 2.4% + $0.30 | 0.5% additional fee |
Stripe's standard rate: 2.9% + $0.30 per transaction (same as Shopify Payments on the Basic plan).
The math for a Basic plan Shopify store:
- Using Shopify Payments on a $100 order: $2.90 + $0.30 = $3.20 in payment fees
- Using Stripe on a $100 order: $2.90 + $0.30 + $2.00 (Shopify transaction fee) = $5.20 in total fees
On the Basic plan, using Stripe costs an extra 2% per transaction — a meaningful cost at any volume. At $50,000/month in revenue, that's $1,000/month extra in fees.
For Shopify merchants: use Shopify Payments.
| Feature | Shopify Payments | Stripe |
|---|---|---|
| Integrated Shopify reporting | Yes (native) | No (separate dashboards) |
| Shopify admin fraud analysis | Yes | No |
| Buy now pay later (Shop Pay Installments) | Yes | Via Afterpay/Klarna integration |
| Shop Pay accelerated checkout | Yes | No |
| Multiple currencies | Yes | Yes |
| Custom checkout | Limited | Full API control |
| Subscription billing | Via Shopify apps | Stripe Billing (native) |
| In-person payments | Shopify POS hardware | Stripe Terminal |
| Marketplace payments (Connect) | No | Yes (Stripe Connect) |
| Platform billing (SaaS revenue) | No | Yes (Stripe Billing) |
Shop Pay is a significant checkout accelerator — it pre-fills checkout for returning Shop Pay users across all Shopify stores, improving conversion. This is unique to Shopify Payments and not available with standalone Stripe.
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Try Sellable free →Stripe's direct use makes sense when: - Building a non-Shopify ecommerce platform or custom checkout experience where Shopify Payments isn't available - Running a SaaS or subscription business where Stripe Billing's subscription management features are needed - Building a marketplace where Stripe Connect handles payments to multiple payees - In-person retail with custom hardware configurations via Stripe Terminal - API-driven payment flows where Shopify's checkout constraints are too limiting
Shopify Payments for any Shopify store — the eliminated transaction fee is a clear economic advantage that outweighs any other consideration.
Stripe for non-Shopify commerce, custom checkout builds, SaaS billing, marketplace payments, and developer-driven payment flows outside of standard ecommerce.
No. Shopify Payments and Stripe are mutually exclusive as your payment processor in Shopify. When Shopify Payments is enabled, Shopify's transaction fee is eliminated. If you add Stripe as an alternative payment method, you pay the transaction fee on Stripe transactions. The best approach is to use Shopify Payments as your primary processor.
No. Shopify Payments is available in approximately 20+ countries (US, Canada, UK, Australia, EU countries, and others). In countries where Shopify Payments isn't available, Stripe is often the recommended alternative. Check Shopify's current list of supported countries for Shopify Payments.
Yes, primarily via Shop Pay. Shop Pay is available only through Shopify Payments and allows returning shoppers to check out in one click using their saved shipping and payment information. Shopify reports Shop Pay has conversion rates 1.72x higher than guest checkout on mobile. This checkout conversion benefit is exclusive to Shopify Payments users.
Payment processor account holds are a real risk for all processors including Shopify Payments. Common triggers: sudden revenue spikes, high chargeback rates, products in restricted categories. If Shopify Payments holds your account, you need a backup payment processor (Stripe, PayPal) ready to activate immediately. Having Stripe as a configured backup payment method in Shopify can prevent revenue loss during a hold.
The chargeback process is similar. Both Shopify Payments and Stripe require you to submit evidence when a customer disputes a charge. Shopify Payments integrates chargeback management into the Shopify admin with a guided response workflow. Stripe's chargeback management is handled in the Stripe Dashboard. For both, maintaining good documentation (shipping confirmation, tracking numbers, customer communications) is the best chargeback defence.
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