Shopify vs Medusa: costs, flexibility and when to choose which

Shopify and Medusa are often compared as if they were two versions of the same product. They are not. Shopify is a hosted SaaS platform: you rent a complete store, including hosting, checkout and admin. Medusa is an open-source commerce engine that you host yourself or run on Medusa Cloud. On top of it you build your own storefront, often in Next.js. That choice determines almost everything: what you pay per month, what you can change yourself and who is responsible when something breaks.

This article compares the two on five points: licence and transaction costs, apps, hosting, cost over three years, and flexibility for B2B, multiple stores and multiple regions. We finish with the situations in which you should simply stay on Shopify.

The comparison in one table

Sources: Shopify pricing (Dutch page) and Medusa pricing, both read on 5 November 2026. Shopify and Medusa list their prices in US dollars. Revenue and payment costs are calculated in euros.

Licence and transaction costs

With Shopify you pay a fixed subscription. The Dutch pricing page lists the amounts in US dollars; converted, Basic costs about €35 per month billed monthly or €26 billed yearly, Grow about €94 or €70 and Advanced about €355 or €266. Shopify Plus starts at €2,050 per month. On 5 November 2026 the pricing page says "from"; the exact amount comes from sales.

The second part of the bill scales with your revenue. If you use Shopify Payments, you pay Shopify's card rates. If you want your own payment provider, for example because your accounting and refunds already run through Mollie or Adyen, Shopify charges a transaction fee on top. That is 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus. With €1 million in annual revenue on Advanced, that is €6,000 a year, just for not using their payment service.

Medusa works differently. The source code is under the MIT licence, except for some Enterprise features such as roles and permissions (RBAC). Self-hosting therefore costs no licence. If you choose Medusa Cloud, you pay €26, €88 or €266 per month for Develop, Launch or Scale. Medusa explicitly adds: 0% GMV fee, unlimited orders, products, sales channels, regions and admin users. You only pay the transaction costs of your own payment provider. At Mollie, on 5 November 2026, that is €0.32 per iDEAL payment and 1.80% + €0.25 for consumer cards from the EEA (Mollie pricing).

How much that can matter is shown by the Healthletic customer story. According to Medusa, Healthletic paid €22,300 per month on Shopify Plus in platform and transaction fees, with more than €21 million in annual revenue across six markets. After the move, "selling more no longer increases the platform bill" (Medusa: Healthletic). That is a large merchant. At €300,000 in annual revenue the difference is much smaller, and the build costs of Medusa weigh more heavily.

Apps and extensions

Shopify has the largest app store on the market. Reviews, subscriptions, bundles, translations: there is an app for almost every need, often installed within an hour. That is a real strength. The downside is in the total. Every app is a separate subscription with its own pricing model, and some charge per order. After a few years many merchants pay more for apps than for Shopify itself. What that is for you, you can read from your own invoices. An honest comparison starts with that total.

Medusa has fewer plugins, and there is no point denying it. What it does have: a modular core with commerce modules for pricing, promotions, inventory, fulfilment, regions, sales channels and tax, among others (Medusa documentation). Whatever is missing, you build as your own module or workflow. That costs one-off development time instead of a monthly fee, and the logic lives in your own code.

Hosting and operations

With Shopify you do not have to think about servers, security updates or traffic peaks. That is included, and for most small and mid-sized stores it is the strongest argument for Shopify.

With Medusa you choose. You host it yourself, for example a Node.js server with Postgres, or you use Medusa Cloud. Medusa Cloud handles infrastructure, previews and scaling. According to Medusa there is no lock-in: you can move to self-hosting later. The storefront usually runs separately, for example on Vercel. That gives freedom, but it also means someone has to look after that stack. Without a developer or agency, Medusa is not a good idea. How we organise that maintenance is described under Medusa maintenance and support.

What does it cost over three years?

An example using published prices only. Revenue is €1 million per year and you use your own payment provider. Apps, build and maintenance are not included, because they differ per project.

On platform costs Medusa clearly wins this example. But the example is incomplete: a Medusa shop has to be built. A storefront, a checkout, integrations with an ERP or WMS and testing all of that cost considerably more up front than a Shopify theme with apps. After that you pay for maintenance on an ongoing basis. The rule of thumb: the higher your revenue and the more you pay for apps today, the sooner Medusa becomes cheaper. For a small revenue with standard products, Shopify is almost always cheaper over three years.

Flexibility: B2B, multiple stores and regions

This is where the biggest functional difference lies. Shopify has B2B features, but up to three B2B catalogues on the regular plans. Unlimited is Plus only. An extensively customised checkout is also a Plus feature, and on the regular plans you get one headless storefront versus 25 on Plus (Shopify pricing). If you want B2B, several brands and your own checkout rules, you quickly end up at the Plus price.

With Medusa, regions, currencies, sales channels, customer groups and price lists are part of the core. You build a B2B portal with quotes, company accounts and approval flows on the same engine as the consumer shop. Medusa maintains an official B2B starter under the MIT licence for this. More on that in our Medusa B2B webshop service.

Medusa's customer stories show where Shopify merchants got stuck:

• Eight Sleep started on Shopify in 2017. According to Medusa, "high costs and limited control over the backend became a bottleneck" with more than ten 3PLs and more than thirty markets. The migration was phased, starting with fulfilment, and finished within four months (Medusa: Eight Sleep).
• Hooch sells printed cans to business customers. On Shopify they could only offer standard products; custom orders went through email and phone. "With Shopify we often needed developers, even for small changes," says their web designer. The new B2B shop with a configurator went live within two weeks (Medusa: Hooch).
• Healthletic moved from Shopify Plus in phases. Old subscriptions and fulfilment stayed in Shopify for a while via a sync plugin. Medusa reports roughly 30% higher checkout conversion in the first month (Medusa: Healthletic).

These are stories Medusa publishes itself, with the figures of Medusa and those customers. They are not Alpha Digital projects. We use them as illustration, not as a promise.

When should you choose Shopify?

Shopify is the better choice if:

• you want to launch quickly and have no long-term developer or agency;
• your assortment is straightforward and you sell B2C without special pricing rules;
• your revenue is below the point where revenue fees and apps start to weigh heavily;
• you see the Shopify checkout and Shop Pay as an advantage, not a limitation;
• you want to connect an in-store POS without any custom work.

In those situations Medusa is mainly more expensive and slower. We say so in an intro call too.

When should you choose Medusa?

Medusa fits if:

• you want B2B and B2C on one system, with your own price agreements per customer;
• you want to manage several stores, brands or countries from one backend;
• your checkout, order flow or fulfilment differs from what a standard platform allows;
• revenue fees and app subscriptions have become a clear cost item;
• you want to own the code and data and be able to switch hosting later.

In doubt? Start with the question of which processes currently live outside the shop: in spreadsheets, emails or separate apps. That list determines the choice more than the platform does. We describe the move itself in Migrating to Medusa. Other comparisons: WooCommerce vs Medusa, Magento vs Medusa, PrestaShop vs Medusa and Lightspeed vs Medusa.

Where Medusa is not the best choice

To be fair:

• Ecosystem. There are fewer ready-made plugins than for Shopify. A new feature is more often development work than a click.
• Your own responsibility. Hosting, updates and monitoring are with you or your agency, also with Medusa Cloud for the backend.
• Start-up costs. A well-built Medusa shop costs more at the start than a Shopify theme.
• Enterprise features. RBAC, SSO and audit logs fall under Medusa Enterprise, which you pay for separately.

Having a Medusa webshop built?

Want to know what it means for your shop? Medusa webshop development explains how we build a new shop, and Migrating to Medusa how we move a Shopify shop without losing traffic. Request a callback or book an intro call.

Sources

Dollar amounts from the sources are converted to euros at the ECB rate of 5 November 2026 (1 euro = 1.1224 US dollars) and rounded.