MedusaJS has emerged as the most compelling open-source alternative to Shopify for headless commerce. Built on Node.js with a modular architecture, it offers the flexibility and control that developers crave — without the licensing fees that eat into margins. But is it the right choice for your business? This comparison examines both platforms honestly, so you can make an informed decision based on your specific requirements.
What Is MedusaJS?
MedusaJS is an open-source, composable commerce engine built with Node.js and TypeScript. It provides the backend infrastructure for eCommerce — product management, cart and checkout, orders, payments, shipping, and customer management — through a modern API. Unlike traditional platforms, Medusa is designed from the ground up to be headless, meaning it has no built-in frontend. You build (or choose) your own storefront using any framework.
The project is maintained by the Medusa team with strong community contributions. It follows a modular architecture where core functionality is provided through modules that can be extended, replaced, or supplemented with custom modules. This makes it remarkably flexible whilst maintaining a clean, well-documented codebase.
MedusaJS vs Shopify: A Head-to-Head Comparison
| Aspect | MedusaJS | Shopify |
|---|---|---|
| Licensing cost | Free (MIT licence) | $39-$399/month (Plus from $2,000/month) |
| Hosting | Self-hosted (Railway, AWS, DigitalOcean) | Fully managed by Shopify |
| Architecture | Headless-native, modular | Monolithic with headless option (Hydrogen) |
| Technology stack | Node.js, TypeScript, PostgreSQL | Ruby on Rails (proprietary) |
| Customisation | Unlimited — full source code access | Limited by platform constraints |
| Plugin ecosystem | Growing (100+ plugins) | Mature (8,000+ apps) |
| Multi-currency | Native support with regions | Shopify Markets (all plans) |
| Transaction fees | None (only payment processor fees) | 0.5-2% unless using Shopify Payments |
| Data ownership | 100% — your database, your servers | Shopify controls the infrastructure |
Total Cost of Ownership
This is where the comparison gets interesting. Shopify's pricing is predictable — a monthly subscription plus transaction fees and app costs. For a mid-market store doing $50,000/month in revenue, expect to pay $300-800/month all-in (platform fees, apps, transaction fees on non-Shopify Payments).
MedusaJS has no licensing fees, but you must account for hosting costs ($20-100/month for a typical setup on Railway or DigitalOcean), potentially higher upfront development costs (since there is no theme marketplace), and the ongoing cost of maintaining the infrastructure. However, the absence of per-transaction fees and monthly app subscriptions means the total cost of ownership often favours MedusaJS once you pass $30,000-50,000 in monthly revenue.
Over a three-year period, a business processing $100,000/month through Shopify (with typical apps and without using Shopify Payments) might pay $40,000-60,000 in platform-related costs. The same business on MedusaJS might spend $15,000-25,000 — but with higher upfront development investment.
Developer Experience
MedusaJS is built by developers, for developers. The codebase is written in TypeScript, uses modern patterns like dependency injection, and follows a clean modular architecture. The API documentation is comprehensive, and the CLI provides scaffolding tools that accelerate development. If your team is comfortable with Node.js and TypeScript, MedusaJS feels familiar and productive.
Shopify's developer experience has improved dramatically with Hydrogen and the Storefront API. The tooling around Liquid themes is mature, and the API surface is well-documented. However, Shopify development often involves working around platform constraints rather than building freely. The Shopify way is opinionated — which is an advantage for speed but a limitation for bespoke requirements.
Flexibility and Customisation
This is MedusaJS's strongest advantage. Because you have full access to the source code, you can customise any aspect of the commerce engine. Need a custom pricing model? Build a pricing module. Want to integrate with a niche ERP system? Write a custom plugin. Need to modify the checkout flow to comply with specific regulatory requirements? You have full control.
Shopify constrains what you can customise. Checkout modifications require Shopify Plus (starting at $2,000/month). The backend logic — how orders are processed, how inventory is managed, how taxes are calculated — follows Shopify's rules. For most businesses, these constraints are perfectly acceptable. But when they are not, working around them can be expensive and fragile.
When to Choose MedusaJS
- You need deep customisation of commerce logic — custom pricing, bespoke checkout flows, unique fulfilment workflows, or complex B2B requirements.
- You want to avoid recurring platform fees and your revenue is high enough that Shopify's percentage-based costs become significant.
- Data sovereignty matters — you need full control over where customer data is stored, which is particularly relevant for EU businesses with strict GDPR requirements.
- You have a capable development team (in-house or agency) comfortable with Node.js, TypeScript, and managing infrastructure.
- You are building a marketplace or multi-vendor platform that requires custom multi-tenancy logic beyond what Shopify supports natively.
When to Choose Shopify
- Speed to market is critical — Shopify can have you selling within days, not weeks. The ecosystem of themes, apps, and payment integrations accelerates launch dramatically.
- You do not have a dedicated development team and want a platform that non-technical staff can manage day-to-day.
- You want managed infrastructure — security updates, SSL, PCI compliance, uptime, and scaling are handled for you with no operational overhead.
- You need specific app integrations that are readily available in the Shopify App Store but would require custom development on MedusaJS.
The Bottom Line
Neither platform is universally better. Shopify excels at reducing complexity and getting you to market quickly with minimal technical investment. MedusaJS excels at giving you total control, eliminating recurring fees, and enabling customisations that would be impossible or prohibitively expensive on Shopify. The right choice depends on your team's technical capabilities, your budget structure (upfront vs. recurring), and how much customisation your business truly requires. At Born Digital, we work with both platforms and can help you make the right decision for your specific situation.