The question comes up for every e-commerce project. Our short answer: it depends. The long answer — it depends on 4 criteria.
1. Catalog complexity
Shopify is great for a standard catalog. For 50,000 references with variants, bundles, configurators and prices per account: Medusa takes the upper hand.
2. Parcours BtoB
Prioritized accounts, quotes, approvals, negotiated prices: Shopify B2B has caught up, but remains limited on truly complex cases. Medusa allows everything, at the cost of a more engaging build.
3. IS integrations
If your ERP dictates prices, inventory and invoicing, Medusa (open-source, API-first) is more flexible. Shopify often requires middleware.
4. Autonomie & lock-in
Medusa = code to you. Shopify = tenant. Both are valid — but the question needs to be asked.