Shopify Plus vs Medusa.js: Which Wins for Enterprise Migration?
Both run serious commerce. The difference is what you pay to grow and what you are allowed to change. Here is the honest comparison of fees, checkout control, and ownership, and when migrating actually pays off.
What does Shopify Plus actually cost at enterprise scale?
Using any non-Shopify payment gateway adds a 0.15%-0.30% surcharge to every transaction. On $10M GMV that is $15,000-$30,000 a year, indefinitely, for using your own processor.
Shopify owns the checkout. Deep customization, custom payment logic, and B2B flows are constrained to what the platform exposes, not what your business needs.
Shopify Plus starts around $2,300/month and rises with GMV. You rent the infrastructure, you never own it, and leaving means rebuilding.
Where does Medusa.js win, and where does Shopify Plus still make sense?
Medusa wins on cost at scale
Medusa.js is open-source with zero licensing or transaction fees. Once your Shopify Plus platform and gateway fees exceed the cost of running an owned stack, Medusa is simply cheaper, and the gap widens as you grow.
Medusa wins on control and ownership
You own the checkout, the data, the roadmap, and the infrastructure. Custom B2B pricing, complex catalogs, ERP-connected inventory, and bespoke checkout logic are build decisions, not platform permissions.
Shopify Plus still wins on speed to launch
If you need to be live in weeks with no engineering team, Shopify Plus is the right call. Its hosted model removes operational overhead that a headless stack asks you to own.
The honest rule of thumb
Migrate when platform plus transaction fees pass roughly $30K-$50K per year, when the checkout blocks revenue you cannot capture, or when you need infrastructure ownership for compliance or an acquisition. Below that, stay on Shopify Plus.
How does Seeed migrate Shopify Plus to Medusa without losing SEO or sales?
Full URL and 301 map, metadata parity, structured data, and SSR/ISR rendering so rankings carry over. We validate parity before cutover, not after.
Your Shopify Plus store keeps selling while we build and validate the Medusa stack. Traffic moves only once the new store matches or beats it.
We connect Square via the @weareseeed/medusa-square-plugin: Apple Pay, Google Pay, and Cash App Pay included, with no platform transaction fee ever again.
“The merchants who win with headless are not chasing a trend. They have done the math. Once your Shopify Plus fees cross what an owned Medusa stack costs to run, staying is the expensive choice.”
Shopify Plus vs Medusa: common migration questions?
The questions enterprise teams ask before committing to a Shopify Plus migration.
Talk to a Solutions Architect
Tell us your current Shopify Plus plan, GMV, and key apps. We will model the migration scope, savings, and timeline, no obligation.
No transaction fees after migration
Square processes at standard rates. No Shopify surcharge ever again.
Full checkout ownership
Medusa checkout is open-source. Build what your business needs.
Zero platform fees forever
Medusa.js is MIT-licensed. Hosting costs replace platform costs.
30-day post-launch support
SEO monitoring, edge case fixes, Search Console management.
Talk to a Solutions Architect
Tell us your current Shopify Plus plan, GMV, and key apps. We will model the migration scope, savings, and timeline, no obligation.
No transaction fees after migration
Square processes at standard rates. No Shopify surcharge ever again.
Full checkout ownership
Medusa checkout is open-source. Build what your business needs.
Zero platform fees forever
Medusa.js is MIT-licensed. Hosting costs replace platform costs.
30-day post-launch support
SEO monitoring, edge case fixes, Search Console management.
