Shopify vs a Custom E-commerce Platform: Plans, Fees, Headless and When Custom Pays

The short answer

Most online shops should start on Shopify and stay there for years. The platform's hosting, checkout, payments, tax, fraud checks and app ecosystem are expensive to rebuild, and a custom build only pays back when your business model does not fit Shopify's shape. The question is not "Shopify or custom" but which of four levels you need.

Shopify plans and fees, checked October 2026

Shopify's US pricing page showed these prices in US dollars on 18 October 2026. Shopify changes prices and runs promotions often, and prices differ by region, so check the page for your country before budgeting.

• Payment processing: Shopify Payments charges card processing fees that depend on your plan and region. If you use a third-party payment provider instead, Shopify adds its own transaction fee on top, which varies by plan; check the pricing page for your region.
• Apps: the real recurring cost for many stores. Subscriptions, reviews, bundles, loyalty and search apps commonly add more each month than the plan itself.
• Themes: free themes exist; premium themes are a one-off purchase.
• Marketplace sales: Shopify's pricing page lists a fee of 1 percent, up to $99 a month, on synced marketplace orders above 50 a month.

Headless: Hydrogen or Next.js in front of Shopify

Headless means keeping Shopify as the commerce engine (products, inventory, checkout, orders) and building your own storefront that reads from the Storefront API. Hydrogen is Shopify's React-based framework for this, hosted on Shopify's Oxygen platform. Next.js with the Storefront API is the common alternative, typically hosted on Vercel, and suits teams that already run Next.js or need the storefront to share code with other web apps.

The trade-off is maintenance. A theme gets Shopify's updates for free; a headless storefront is your code, and every new Shopify feature has to be wired in. Go headless for a measurable reason: page speed on a content-heavy catalogue, a product experience a theme cannot deliver, or one front end across several back ends.

An example of a custom experience that does not need a custom store: AutoViz is a B2B SaaS that gives aftermarket wheel brands an embeddable 3D and AR configurator for their e-commerce sites, with a vanilla JavaScript SDK, WebXR on Android and Quick Look on iOS, and white-labelled builds per brand. It is live for brands including Amani Forged, Variant Wheels and Azara. An embeddable component like this plugs into whatever store a brand runs, so the brand keeps its existing platform and still gets a product experience a theme cannot deliver.

When a custom platform is worth it

• Multi-vendor marketplace: sellers onboard, list and get paid out, with commissions and split payments. Shopify is built for one merchant; marketplace apps exist but strain at scale. See marketplace development and Stripe Connect for marketplaces.
• Rentals, bookings and time-based inventory: availability calendars and deposits do not map onto products and variants.
• Complex B2B pricing: customer-specific price lists, quote approvals, credit terms and ERP-driven stock beyond what Plus B2B handles.
• Configured or made-to-order products where price depends on many options and rules.
• Commerce as one feature inside a larger product, such as a SaaS that sells add-ons or a platform with its own accounts and roles.

For these, the usual architecture is Next.js on the front end, a Node.js or Python API, PostgreSQL, Stripe for payments (Stripe Connect for marketplaces) and a search service. Our calculator puts an Etsy-style marketplace MVP at $38k to $69k and 11 to 21 weeks; open the preset to change the scope, and read cost to build a marketplace app like Etsy for the line-by-line breakdown.

A decision checklist

How we help

We customise Shopify themes and apps, build headless storefronts and build custom commerce platforms; our e-commerce development page covers each, and you can hire Shopify developers at $4,000 to $6,600 a month for seniors. The e-commerce industry page lists related work.

Total cost over three years: a worked comparison

Plan fees are the smallest part of the comparison. A brand on Shopify Advanced pays $299 a month billed yearly, about $10,800 over three years, plus apps and payment fees. A headless storefront adds a custom build and its upkeep. A custom marketplace adds the whole platform, then hosting, payments and an engineering team to keep improving it.

If a custom platform does not open revenue that Shopify cannot (seller commissions, bookings, B2B contracts), it is hard to justify on cost alone. When it does, the platform is the business, and the engineering cost belongs in the business plan, not the marketing budget. Our marketplace app development cost guide shows how marketplace budgets break down.

Migrating off Shopify, or onto it

• Export products, customers and orders through the Admin API rather than CSV when volumes are large; CSV loses metafields and variant detail.
• Keep every product and collection URL or redirect it; e-commerce sites lose more search traffic to broken URLs than to any platform difference.
• Plan customer accounts carefully: passwords cannot be exported, so customers will need to reset or use a magic link.
• Run both systems in parallel for a short period and reconcile orders and stock daily until you switch.

Sources

• Shopify pricing (US): https://www.shopify.com/pricing (checked 18 October 2026)
• Shopify Help Center, third-party payment providers: https://help.shopify.com/en/manual/payments/third-party-providers (checked October 2026)
• Shopify developer docs, Hydrogen deployments: https://shopify.dev/docs/storefronts/headless/hydrogen/deployments (checked October 2026)