Shopify Payments vs Stripe: what's the difference and which should you choose?

Stripe vs Shopify Payments isn't a real choice on Shopify in Belgium and the Netherlands: as long as Shopify Payments is available, you can't connect Stripe as a separate payment provider. Shopify Payments itself runs on Stripe technology, at Shopify's fees. Stripe mainly makes sense for what happens outside your Shopify checkout.

Below you read how the two relate, what they cost and when you do need Stripe. The bigger picture is in our guide to Shopify payments in Belgium and the Netherlands. Fees checked November 2026.

What's the difference between Shopify Payments and Stripe?

Shopify Payments is Shopify's built-in payment solution. Behind the scenes Stripe processes the payments as payment processor. You only see Shopify: you activate it in your admin, and payouts, refunds and chargebacks sit next to your orders.

Stripe is also a standalone payment provider with its own dashboard and API. Companies use Stripe for custom platforms, subscriptions, SaaS and marketplaces. On Shopify in Belgium and the Netherlands, Stripe only works through Shopify Payments, not as a separate provider.

Can you use Stripe on Shopify in Belgium or the Netherlands?

Not as a separate card processor. Shopify only shows Stripe as an option in countries where Shopify Payments doesn't exist. Shopify Payments has been available in the Netherlands since 2019 and in Belgium since 2020, so you won't see Stripe in the list of payment providers there. A Shopify staff member confirmed this in the Shopify Community for a Dutch store.

What does exist: apps that build their own payment page with Stripe, separate from the Shopify checkout. Be careful with those. You lose features of the Shopify checkout, such as Shop Pay and checkout extensions, and you carry more responsibility for the payment flow yourself. We rarely recommend it.

Shopify Payments vs Stripe: the fees side by side

Shopify Payments charges per Shopify plan. Stripe charges one standard rate, regardless of your platform. These are the Belgian fees, checked in October and November 2026.

On paper Stripe is cheaper for European cards. You can't use that difference on Shopify, because you can't pick Stripe there separately. So compare Shopify Payments with the alternatives that do work, as in our comparison Shopify Payments vs Mollie. What you pay in your case, you calculate with our payment simulator for Shopify.

When is Stripe the right choice?

You sell outside Shopify: a SaaS, a booking platform, a marketplace or your own app.

You need complex subscriptions or invoicing, for example with Stripe Billing.

You build a headless frontend and want your own checkout. Even then we recommend the Shopify checkout. Why, you read in our comparison of headless Shopify vs Liquid.

Your store is based in a country where Shopify Payments doesn't exist. Then you do see Stripe as a provider in your admin.

For a regular Shopify store in Belgium or the Netherlands, Shopify Payments is almost always the logical choice: no extra transaction fees from Shopify, Bancontact and iDEAL | Wero built in, and everything in one admin. Unsure between providers in general? Read our guide to the best payment provider for Shopify.

What if you already have a Stripe account?

Many brands already use Stripe for another channel, such as a subscription service or a B2B portal. You don't connect that account to your Shopify checkout. You then run two payment environments: Shopify Payments for the store and Stripe for the rest. Make sure your accounting recognises both payouts separately, because they arrive in different streams. What Shopify costs in total, you read in our guide to Shopify costs and pricing.

What we learned in the Shopify Community

Stripe isn't among the payment providers. Problem: a Dutch merchant wants to connect Stripe but can't find it in the settings. Solution: a Shopify staff member explains that Stripe is only available where Shopify Payments doesn't exist, and that you can't switch off Shopify Payments to pick Stripe. Replies from December 2024 report the same. Our take: in Belgium and the Netherlands you plan with Shopify Payments or a provider such as Mollie. Source: Shopify Community thread (2022, latest replies December 2024).

iDEAL gone, so Stripe? Problem: a Dutch merchant loses iDEAL through Shopify Payments after changed eligibility criteria. Solution: Shopify support points to an external provider such as Mollie, others suggest checkout apps built on Stripe. Our take: choose a provider that works inside the Shopify checkout and count the extra Shopify fee. Source: Shopify Community thread (September 2025 to May 2026).

How 6th Man helps

We set up Shopify Payments at every launch and look at which payment methods your customers actually use. If a platform on Stripe runs next to your store, we make sure both work side by side and arrive correctly in your accounting. See how we build custom Shopify stores.