Medusa vs Shopify Plus: which is better for B2B?

When Shopify Plus is enough

Within a week, Shopify Plus covers around 80% of what a typical DTC store needs: hosting, checkout, peak-season scaling and the app ecosystem. It also has native B2B features such as customer-specific catalogues, company accounts and order limits. If your business model fits those assumptions, headless is a more expensive way to reach the same result.

The limits usually show up in three places. The first is custom pricing logic: B2B, contract prices, several regions. The second is revenue-based fees at high GMV. The third is apps that almost do what you need, each one adding to your maintenance cost.

Where Medusa.js lowers cost per order

Medusa.js is an open backend and the code is yours. You design the data model around your own processes: contract price lists, credit limits, order approval or ERP sync. Above a few tens of millions in annual GMV, the difference in platform fees alone can pay for a team.

The second effect shows later. The roadmap no longer depends on platform limits, so a new sales channel or an A/B test takes days instead of waiting for next quarter.

What Medusa.js does not solve on its own

With headless, responsibility for checkout, infrastructure and monitoring moves to you or to a partner who stays with the project after launch. Without a strong team or that kind of partner, total cost usually goes up.

So before choosing a platform, it is worth settling who will run the store after go-live.

Making the decision

Stay on Shopify Plus if your store fits its model and the fees are reasonable. Choose Medusa.js if custom logic (especially B2B pricing) and unit cost are real constraints, and someone in your team or at a partner will own operations. The cheapest way to decide is to run your own numbers through an audit first.