Merchant Problem Center
Last updated: June 25, 2026
Quick Answer
Shopify Payments is the default payment processor built into Shopify, but it is unavailable in many countries and restricted for certain business types. When merchants use a third-party processor instead of Shopify Payments, Shopify charges an additional transaction fee — 2% on the Basic plan, 1% on Shopify, and 0.5% on Advanced Shopify — on top of the processor's own fees. Understanding this cost structure is critical before choosing an alternative.
In this article
Merchants seek Shopify Payments alternatives for several reasons: geographic unavailability (Shopify Payments is only offered in select countries), business type restrictions, and preference for processors with better pricing, support, or capabilities.
Before choosing an alternative, understand Shopify's transaction fee structure. When you use any payment provider other than Shopify Payments, Shopify adds a fee on every sale — layered on top of whatever the processor charges.
The Shopify transaction fee is the most important factor when evaluating alternatives. On the Basic Shopify plan ($39/month), using a third-party processor adds 2% to every transaction on top of the processor's rate. On a typical 2.9% + $0.30 online rate, your effective cost per transaction could reach 4.9% + $0.30.
For higher-volume merchants, upgrading to a higher Shopify plan to reduce the transaction fee is often more cost-effective than accepting a high additional fee on the Basic plan. At $10,000/month, the difference between a 2% and 0.5% transaction fee is $150/month — potentially exceeding the plan upgrade cost.
Note: Always calculate total cost of processing — processor fee + Shopify transaction fee — before choosing a Shopify alternative. The cheapest processor is not always cheapest when Shopify's fee is included.
Shopify supports hundreds of payment gateways. The major options with strong Shopify integrations include:
Note: Shopify's transaction fee applies to all third-party processors regardless of which one you choose. The fee is determined by your Shopify plan, not by the processor.
Evaluating a Shopify alternative requires looking at total cost — not just the processor's advertised rate. Run the numbers for your specific volume and average transaction size.
Switching payment processors on Shopify is straightforward technically, but plan for potential disruption to recurring billing and pending transactions.
Merchants switching away from Shopify Payments often underestimate the true cost of alternative processors. Avoid these common mistakes.
After switching payment processors on Shopify, a few situations warrant immediate contact with your new processor or Shopify support.
Note: Always confirm the integration is live with a small test transaction before directing real customer traffic through the new processor.
Yes. Shopify charges a transaction fee — 2%, 1%, or 0.5% depending on your plan — on every sale processed through a third-party payment provider. This fee is in addition to the processor's own rates. The only way to avoid Shopify's transaction fee is to use Shopify Payments.
Yes, Stripe integrates natively with Shopify as a third-party payment gateway. However, Shopify's transaction fee still applies when using Stripe. Shopify Payments is powered by Stripe on the backend in some regions, but they are separate products with separate fee structures.
Total cost depends on your Shopify plan, processing volume, and average transaction size. For most merchants, Shopify Payments (if available) is cheapest because it avoids the Shopify transaction fee entirely. Among third-party alternatives, interchange-plus processors like Helcim may be cheapest for higher-volume merchants who can absorb the transaction fee.
No — Shopify Payments is only available in specific countries. If you are in an unsupported country, you must use a third-party payment provider. Check Shopify's current documentation for the complete list of supported countries.
If you use Shopify Subscriptions or a third-party subscription app, card tokens may not transfer between processors. Customers may need to re-enter payment information after the switch. Plan your migration timing carefully and notify subscribers in advance.
Shopify Payments is the only provider that avoids the Shopify transaction fee. All other payment providers, regardless of how they integrate with Shopify, are subject to the transaction fee based on your plan.
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