Shopify Payments and Stripe look similar on the surface — both powered by Stripe's infrastructure — but the fee structures are meaningfully different for Shopify merchants.
The core difference: the Shopify gateway surcharge
If you use Stripe directly on Shopify (not Shopify Payments), Shopify charges an additional transaction fee on top of Stripe's fees: - Basic plan: +2.0% - Shopify plan: +1.0% - Advanced plan: +0.5%
This makes Stripe significantly more expensive for Shopify merchants than Shopify Payments.
Rate comparison: Shopify Payments vs Stripe on Shopify
For a Basic Shopify store ($39/mo) at $10,000/month volume:
| Option | Processing fee | Gateway fee | Monthly total |
|---|---|---|---|
| Stripe on Shopify | $320 | +$200 (2%) | $520 |
| Shopify Payments Basic | $225 | $0 | $225 |
Shopify Payments saves $295/month at $10k volume — easily covering the $39/mo plan cost.
When Stripe outside Shopify is better
If you're not selling on Shopify, Stripe is the better choice: - Better APIs for custom checkout - Superior subscription billing - Better international coverage - No platform dependency
Compare the exact fees for your transaction amounts with our Payment Fee Comparison.