Should I use Shopify or build a custom store?

Shopify or a custom store: the three real options

"Custom store" rarely means writing commerce from scratch. A technical founder launching a DTC brand is choosing between three options:

Hydrogen is Shopify's headless toolkit for building your own storefront, and Oxygen is Shopify's storefront hosting. Shopify's developer docs say Oxygen is available at no extra charge on paid plans. Hydrogen changes the frontend only: products, checkout, plan fees, and apps stay on Shopify.

Medusa is an open source commerce platform (MIT, except its Enterprise Edition RBAC and SSO features) with a framework for custom modules, workflows, and API routes. It ships commerce modules for products, carts, orders, pricing, inventory, and payments, plus an admin dashboard. You host it yourself or on Medusa Cloud.

When Shopify is the right call

Shopify is the better choice for many DTC launches. Stay on Shopify if most of these are true:

• You have no developer on the team and don't plan to hire one.
• Your catalog and checkout are standard: physical products, fixed prices, normal shipping.
• Speed to first sale matters more than control, and you want themes, POS, and marketplace channels on day one.
• You are fine using Shopify Payments, which avoids Shopify's third-party transaction fee.
• Your app needs are covered by free or low-cost apps.

A Medusa build costs developer time before the first order. If the business is still validating demand, that time is usually better spent on product and marketing.

When a Medusa store is the better fit

Medusa fits when the differentiator lives in the backend logic, not just the design:

• Custom product logic: configurators, bundles with separate fulfillment, rentals, or pre-orders. Medusa has official tutorials for each.
• Subscriptions without per-transaction app fees: the subscriptions recipe builds renewals as a custom module, so there is no app-level fee per renewal.
• Owning your data and code: Medusa Cloud lets you export your data and move to self-hosting later.
• Checkout control: you build the checkout and choose payment providers. On Shopify, full checkout customization is listed for Plus only, and only Plus stores can use custom apps that contain Shopify Functions.
• AI and agent features: you can add custom API routes and workflows for agents to call.
• Multiple brands or regions from one backend, with sales channels and regions unlimited on every Medusa Cloud plan.

3-year cost comparison

Platform numbers below are list prices as of October 2026, from Shopify pricing (monthly billing) and Medusa Cloud pricing. Developer time is a variable you fill in, because it depends on your team and scope.

A worked example from the rates above: on $1M of yearly sales through a third-party payment provider, Shopify Advanced's 0.6% fee is $6,000 a year, or $18,000 over three years. Yearly billing lowers Shopify Advanced to $299 a month. App costs are covered in the related entry on Shopify app costs.

The comparison usually turns on D2 versus D1 plus app fees. If D2 is large and your apps are cheap, Shopify wins. If you pay several percentage-based apps or Plus fees, the platform savings can cover the build.

What a migration from Shopify to Medusa looks like

Starting on Shopify does not lock you in. Medusa's Docs MCP server has a Shopify migration tool that gives your AI agent a migration plan for products, variants, prices, images, inventory levels, collections, and categories. It supports an API-based import that can be re-run and a faster CSV approach.

Healthletic, a supplements brand with $24M+ in yearly GMV, moved from Shopify Plus to Medusa with the Medusa Expert partner Rigby. According to Medusa's Healthletic case study, it had paid $25,000 per month in Shopify platform and transaction fees, and checkout conversion was around 30% higher in the first month after migrating. Shopify stayed in place for existing subscriptions and fulfillment during the first phase.