Medusa vs Shopify: Cost, Control and Fit

Medusa vs Shopify is a choice between renting a finished store and owning the engine of one. Shopify is a hosted platform: you pay a monthly plan and get hosting, checkout, admin, security and an app store, all run by Shopify. Medusa is an open-source commerce engine: a TypeScript backend with an admin dashboard that a development team builds your storefront and business logic on. Shopify gets a standard store selling fast with little technical effort. Medusa gives you full control over how the store works, at the cost of building and maintaining it.

We build on both. We’re a Shopify agency for store builds, migrations and growth, and we do Medusa.js development for custom commerce. Our own Medusa page says plainly that for a standard direct-to-consumer catalogue, Shopify’s app ecosystem and managed infrastructure are genuine advantages. This guide covers where each platform wins, what each really costs, and when moving from Shopify to Medusa makes sense.

Medusa vs Shopify at a Glance

Short answer: stay on Shopify if you sell a standard catalogue and want your team running the store, not maintaining software. Choose Medusa when your commerce logic, such as B2B pricing, marketplaces, unusual checkout rules or multiple channels, is something Shopify can’t support without workarounds, and you have developers to build and look after it.

What Each Platform Is

Shopify is software as a service. You sign up, choose a plan, pick a theme and start selling. Shopify runs the servers, the checkout, payment processing (through Shopify Payments where it’s available), security updates and traffic peaks. You customize the store through themes, settings and apps, but you never touch Shopify’s core code.

Medusa is a commerce engine you deploy. It provides the building blocks of a store: products, carts, orders, customers, pricing, regions, payments and fulfillment. It exposes them through APIs, and Medusa Admin gives your team a dashboard to manage them. There’s no finished storefront. A developer builds one, usually starting from Medusa’s Next.js starter storefront, and writes the custom logic your business needs as modules, workflows or API routes. The code is MIT-licensed, so you can run, change and host it however you like.

So the comparison isn’t really “paid platform vs free platform”. It’s a subscription product with costs you know in advance against a software project that you, or your agency, own and run.

Who Runs the Store: Ease of Use and Admin

On Shopify, a non-technical team handles nearly everything: products, collections, discounts, orders, refunds, shipping rates, taxes and theme changes. Most new needs are met by installing an app. Shopify’s admin and mobile app are polished, and staff can be trained quickly.

On Medusa, daily operations also happen in a dashboard. Medusa Admin covers products, inventory, orders, customers, pricing and promotions. The difference shows when something new is needed. A new payment method, a pricing rule, a storefront section or an integration with your ERP is development work, not an app install. Medusa Admin can be extended with custom pages and widgets, but someone has to build them.

The practical question is whether you have, or want, a lasting development relationship. With Shopify, you can run a store for years without a developer. With Medusa, you shouldn’t try.

Customization and Checkout

This is where the platforms differ most.

Shopify gives you a lot of room on the storefront. Liquid themes can be customized heavily, and Hydrogen, Shopify’s React framework, lets you build a fully custom headless storefront hosted on Shopify’s Oxygen platform. The backend and checkout are Shopify’s. You extend them with:

• Checkout Extensibility: apps and checkout UI extensions that add fields, content and upsells at set points in the checkout. Customizing the information, shipping and payment steps is limited to Shopify Plus.
• Shopify Functions: small pieces of logic that run inside Shopify for discounts, delivery and payment options, cart validation and similar rules.
• Shopify Scripts, now retired: Scripts were Shopify Plus’s older way to customize checkout logic. As of October 2026 they’re gone. Shopify stopped allowing edits on April 15, 2026 and stopped running Scripts on June 30, 2026. Their logic has to be rebuilt with Functions.

That model is safe and fast, but it’s bounded. You change checkout where Shopify allows it, in the way Shopify allows it.

Medusa has no such boundary. The cart, checkout and order logic is code you control. Custom pricing per customer group, quote-to-order flows for B2B, multi-vendor order splitting, conditional payment methods, rental or deposit logic: you build the rule exactly as the business needs it. The trade-off is that you build it, test it and maintain it. For a deeper look at what’s possible, see Medusa checkout customization.

Apps vs Modules: Integrations

Shopify’s App Store is its biggest advantage for most merchants. Reviews, subscriptions, loyalty, returns, email marketing, product feeds, ERP and accounting connectors, and much more are usually a few clicks away. The downsides are recurring app fees that add up, apps that overlap or conflict, and storefront speed that suffers as scripts pile up.

Medusa’s ecosystem is smaller and more technical. Integrations come as modules and providers: payment (Stripe has an official module), fulfillment, notifications, search, file storage and CMS connectors. Anything that doesn’t exist yet is written against Medusa’s APIs. You get integrations that fit your exact process and no per-app subscriptions, but every integration is development time.

If your business runs well on off-the-shelf apps, that’s a strong reason to stay on Shopify. If you’re already paying developers to work around app limitations, that’s a reason to look at Medusa.

Frontend, Design and SEO

Shopify themes give you a professional storefront quickly, and a custom theme can match almost any brand. Hydrogen goes further for teams that want a React storefront. Shopify handles core SEO well: editable titles and meta descriptions, sitemaps, canonical tags and fast hosting. It also sets some rules you can’t change, such as fixed URL patterns like /products/ and /collections/.

Medusa has no theme layer. The storefront is a separate application, typically Next.js, so design, page structure, URLs, rendering and structured data are entirely up to you. That freedom helps when content and commerce need to live together or when SEO requirements are specific. It also means SEO is only as good as the team that builds and maintains the frontend. See Medusa storefront options for the common approaches.

Neither platform is better for SEO by default. Shopify gives you good defaults with fixed limits. Medusa gives you no defaults and no limits.

Hosting, Security and PCI

Shopify hosts everything. Uptime, scaling for sales peaks, security patches and PCI DSS compliance for its checkout are Shopify’s job. For most merchants, not having to think about infrastructure is a real, if invisible, benefit.

Medusa runs wherever you deploy it: your own cloud infrastructure, or Medusa Cloud, the company’s managed hosting. The backend, database, storefront hosting, backups, monitoring and updates are your responsibility, or your agency’s. On payments, card details are usually collected by the payment provider’s own hosted fields (for example Stripe’s), so card data doesn’t touch your servers and most of the PCI burden stays with the provider. You’re still responsible for securing the servers, the admin and your custom code.

Real Costs

Both platforms pay a payment processor on every sale. Card processing fees exist on Shopify and on Medusa (through Stripe, for example), so they aren’t a Shopify-only cost. What differs is everything around them.

Shopify plans (as of October 2026, US pricing; source):

The extra fee in the last column applies only when you process payments through a third-party gateway instead of Shopify Payments. Shopify Payments isn’t available in every country, so for some stores this fee is unavoidable. On top of the plan, most Shopify stores pay monthly app subscriptions, plus theme or development costs.

Medusa costs (as of October 2026; source):

• Software: free and open source (MIT). No platform fee on sales.
• Hosting: self-host on your own infrastructure, or use Medusa Cloud. Its plans are Develop ($29/month), Launch ($99/month), Scale ($299/month) and custom Enterprise, with no fee on GMV. Your storefront hosting, and often a CMS and a search service, come on top.
• Development: this is the main cost. The storefront, integrations and custom logic are built rather than installed, and the store needs ongoing developer time for updates, fixes and new features.

The honest summary: Shopify’s costs are predictable and grow with the plan you need, the apps you add and, without Shopify Payments, your sales. Medusa’s software and hosting are cheap. Its real cost is development, upfront and ongoing. Medusa saves money when it removes app subscriptions, workarounds and platform limits that are already costing you. It costs more when you’d simply be rebuilding what Shopify gives you out of the box. Our Medusa total cost of ownership guide goes through the line items.

When Shopify Is the Better Choice

• You sell a standard catalogue. Products, variants, discounts, shipping and a clean checkout are what Shopify does best.
• A non-technical team runs the store. Shopify lets them work without waiting on developers.
• You want to launch quickly. A Shopify store can be selling far sooner than a custom build.
• Apps cover your needs. If the App Store already solves your problems, there’s no case for rebuilding them.
• You’d rather not own infrastructure. Hosting, security and scaling stay Shopify’s job.

This is the position our own Medusa development page takes: for a standard direct-to-consumer catalogue, Shopify’s app ecosystem and managed infrastructure are genuine advantages, and Medusa is worth evaluating only when the platform starts limiting the business. If that’s you, our Shopify agency work is where to start.

When Medusa Makes Sense

• Your commerce logic doesn’t fit Shopify. Customer-specific pricing, quotes and approvals, multi-vendor marketplaces, rentals, deposits or complex bundles. See Medusa for B2B commerce and Medusa marketplace builds.
• Checkout has to work your way. You need rules that checkout extensions and Functions can’t express.
• You sell across regions and channels from one backend. Medusa treats regions, currencies and sales channels as core concepts.
• Commerce is part of a larger product. Medusa’s APIs plug into an existing app or platform rather than standing alone.
• You want to own the code and data. No platform can change your checkout, deprecate a feature you rely on, or change your terms.
• You have developers, or a committed agency. Medusa needs ongoing technical attention.

If several of these apply, that’s where Medusa.js development earns its cost.

What about WooCommerce? If what you mainly want is open-source ownership with a content-led store that a non-developer can run, WooCommerce sits between the two. It’s open source, runs on WordPress and has a large plugin ecosystem, but you host and maintain it. We compare it in Medusa vs WooCommerce and build it through custom WooCommerce development.

Moving From Shopify to Medusa

Moving from Shopify to Medusa is a rebuild of the store’s behaviour plus a migration of its data. In outline:

What moves:

• Products, variants and collections: exported from Shopify (CSV or the Admin API) and mapped to Medusa’s products, options and categories.
• Customers and addresses: exported and imported through Medusa’s APIs.
• Order history: imported for customer accounts and reporting, or kept as a read-only archive with live orders starting in Medusa from a cutover date.
• URLs: every indexed product, collection, page and blog URL mapped to its new address and 301-redirected.

What gets rebuilt:

• The storefront, cart, checkout and account pages.
• Everything your apps did: reviews, subscriptions, loyalty, emails, feeds and integrations.
• Any Scripts or Functions logic, rewritten as Medusa code.

What needs a plan:

• Passwords: Shopify doesn’t export customer passwords, so customers set a new one on first login.
• Saved payment methods and subscriptions: these usually don’t transfer automatically. Check with your payment provider and subscription app before planning renewals.
• SEO: carry over titles, meta descriptions and content, and watch Search Console after launch.

For the full process, read our guide to migrating from Shopify to Medusa. If you’re on Shopify Plus, see Medusa vs Shopify Plus as well.

Frequently Asked Questions

Is Medusa cheaper than Shopify?

The software is. Medusa is free and open source, and Medusa Cloud starts at $29/month with no fee on sales (as of October 2026). But Medusa needs a storefront and custom features to be built and maintained, so development is the main cost. Medusa ends up cheaper when it replaces app fees, gateway fees and workarounds that are already expensive. For a standard store, Shopify is usually cheaper overall.

Is Medusa free?

The code is free under the MIT license, and self-hosting has no license fee. You still pay for hosting (your own or Medusa Cloud), a storefront host, any third-party services, and developer time.

Can Medusa replace Shopify Plus?

For businesses whose needs go beyond what Shopify Plus allows, such as custom checkout logic, B2B workflows or marketplaces, yes. Medusa handles that logic natively. You take on hosting and maintenance that Shopify Plus includes, so it suits teams with developers or a long-term agency partner.

Can I migrate from Shopify to Medusa?

Yes. Products, customers and order history can be migrated, and URLs can be 301-redirected to protect SEO. The storefront, checkout and app functionality have to be rebuilt. Customers will need to reset their passwords, and saved payment methods need a plan.

Do I need developers to run Medusa?

Not for daily operations. Medusa Admin handles products, orders, customers and promotions. Anything new, such as a payment method, a pricing rule, a storefront change or an integration, needs a developer. Plan for an ongoing development relationship.