Ecommerce Without Shopify: How to Own Your Entire Stack

Shopify powers millions of stores, but it is not the only option — and for growing businesses, it is increasingly not the best option. Running ecommerce without Shopify means owning your code, your data, and your customer relationships without a platform taking a cut of every sale. No transaction fees skimming your margins. No app subscriptions draining your budget. No vendor lock-in trapping you in a walled garden when you outgrow the platform's limitations.

The question isn't whether you can run an online store without Shopify — thousands of businesses already do. The real question is which alternative fits your technical capabilities, your growth plans, and your tolerance for managing your own infrastructure. This guide breaks down every viable option, from traditional self-hosted WooCommerce to modern headless commerce architectures.

Why stores are moving away from Shopify

Shopify's appeal has always been simplicity. Sign up, pick a theme, add products, and you're selling. But that simplicity comes with costs that compound as your store grows — costs that push an increasing number of merchants to look for alternatives.

Transaction fees that scale with revenue. Unless you use Shopify Payments (which isn't available in every country and locks you into their payment processing), Shopify charges 0.5-2% on every transaction on top of your payment gateway's own fees. For a store doing $500,000 per year, that's $2,500-10,000 in platform fees alone — money that goes directly to Shopify for the privilege of using their checkout.

App ecosystem costs. Shopify's core feature set is deliberately limited to drive merchants into their app marketplace. Need product reviews? That's an app. Subscription billing? An app. Advanced shipping rules? Another app. The average Shopify store runs 6-8 apps, and the average annual spend on apps ranges from $462 to $800 per year — and that's for small to mid-size stores.

Limited customisation. Shopify uses Liquid, a proprietary templating language that most developers find frustrating compared to modern frameworks like React or Vue. Checkout customisation is locked down on all plans except Shopify Plus ($2,300+/month), and even then your options are constrained compared to what you can build on an open platform. When you hit a wall with Shopify's architecture, there's often no way around it.

Vendor lock-in. Your store, your customer data, your order history — it all lives on Shopify's servers. While you can export basic CSV files, there's no guarantee you can move your entire store without significant data loss and manual rework. Shopify has no incentive to make migration easy, and the longer you stay, the harder it gets to leave. For a detailed breakdown of the financial side, see our guide on why Shopify is too expensive for growing stores.

The alternatives that actually work

Not every Shopify alternative is worth your time. Some are just different flavours of the same SaaS lock-in problem (BigCommerce, Squarespace). Others are genuinely different architectures that give you ownership and control. Here are the options that matter.

WooCommerce (self-hosted WordPress)

WooCommerce is the most popular alternative to Shopify by a significant margin. It powers over 40% of all ecommerce sites on the web — more than Shopify, Magento, BigCommerce, and Squarespace combined. It's a free, open-source plugin that turns any WordPress site into a fully-featured online store.

The strengths are obvious: zero licensing fees, a massive plugin ecosystem with thousands of extensions, built-in WordPress content management for blogs and landing pages, and complete ownership of your data. You can run WooCommerce on any hosting provider, switch hosts whenever you want, and customise every aspect of the platform without asking permission.

The weakness is equally obvious: WooCommerce runs on PHP, and a traditional WordPress frontend is slower than Shopify out of the box. Without proper caching, optimisation, and hosting configuration, WooCommerce sites can feel sluggish — particularly on product pages with complex variations. This is a solvable problem, but it requires technical knowledge that many store owners don't have.

Headless WooCommerce + Next.js

This is where things get interesting. Headless WooCommerce takes everything good about WooCommerce — the backend operations, the plugin ecosystem, the payment gateway integrations, the admin interface — and replaces the slow PHP frontend with a modern Next.js application built in React.

The result is Shopify-level speed (or better) with full ownership of your stack. Your frontend is edge-deployed on Vercel or Cloudflare, your product pages load in milliseconds, and your checkout experience is completely custom. You get the best of both worlds: WooCommerce's mature ecosystem and Next.js's modern performance. For a deep dive, read our guide on what headless WooCommerce is and how it works.

Medusa (Node.js headless commerce)

Medusa is an open-source, TypeScript-based headless commerce platform built specifically for developers. It's modular, extensible, and designed from the ground up for headless architectures. If your team is comfortable with Node.js and wants to build a commerce backend from composable modules rather than adapting an existing system, Medusa is a compelling option.

The trade-off is ecosystem size. Medusa is newer and smaller than WooCommerce, which means fewer pre-built integrations, fewer community resources, and more custom development for features that would be a plugin install on WooCommerce. For developer-heavy teams building bespoke commerce experiences, that's fine. For everyone else, it's a significant consideration.

Saleor (Python/GraphQL headless commerce)

Saleor is an enterprise-grade, open-source headless commerce platform built with Python and Django, featuring a GraphQL-first API. It offers strong multi-channel, multi-currency, and multi-warehouse support out of the box — capabilities that typically require expensive Shopify Plus add-ons or custom WooCommerce development.

The downside is complexity. Saleor has the steepest learning curve of any option on this list, the smallest ecosystem, and requires Python expertise for backend customisation. It's best suited for enterprise teams with dedicated development resources. For a detailed comparison, see headless WooCommerce vs Medusa vs Saleor.

What you gain by owning your stack

Moving away from Shopify isn't just about avoiding fees — it's about gaining capabilities that a SaaS platform will never give you. When you own your stack, every decision about your store's technology is yours to make.

These aren't theoretical advantages. For a store doing $1 million in annual revenue, eliminating Shopify's 2% transaction fee alone saves $20,000 per year. Add in app subscription savings and the elimination of platform-imposed limitations, and the financial case for owning your stack is overwhelming at scale.

What it takes to run your own stack

Ownership comes with responsibility. Running your own ecommerce stack means you're responsible for things that Shopify handles for you. That doesn't make it harder — it just means the work shifts from writing cheques to a SaaS provider to managing (or hiring someone to manage) your own infrastructure.

Hosting management ($25-100/month). You need reliable hosting for your WooCommerce backend and, if going headless, a frontend deployment platform like Vercel. The good news: quality managed WordPress hosting from providers like Cloudways or GridPane costs a fraction of what Shopify charges in transaction fees alone.

Security updates and maintenance. WordPress core, WooCommerce, and your plugins need regular updates. Managed hosting providers handle much of this, but you need a process for testing updates before they go live and responding quickly if something breaks.

Payment gateway setup. Instead of being locked into Shopify Payments, you connect directly to Stripe, PayPal, or any gateway you choose. The setup is straightforward — WooCommerce has official plugins for every major payment provider — but you're responsible for ensuring PCI compliance and handling any gateway-specific configuration.

The practical path: from Shopify to headless WooCommerce

If you're currently on Shopify and want to move to a self-hosted stack, the migration process is well-documented and manageable. Here is what the path looks like at a high level.

Step 1: Export your data from Shopify. Products, orders, customers, and discount codes can all be exported as CSV files. Shopify also provides an API for more comprehensive data extraction. The key is to export everything before you cancel your Shopify subscription — once your account is deactivated, your data access becomes limited.

Step 2: Set up your WooCommerce backend. Install WordPress on your chosen hosting provider, add WooCommerce, and import your product catalogue. WooCommerce has built-in CSV importers, and there are dedicated Shopify-to-WooCommerce migration plugins that handle the mapping automatically.

Step 3: Build or deploy your headless frontend. If you're going headless, this is where you set up your Next.js frontend, connect it to WooCommerce via the REST API or WPGraphQL, and build out your product pages, category pages, cart, and checkout. For a complete walkthrough, see our WooCommerce to headless migration guide.

Step 4: Set up 301 redirects. Map every Shopify URL to its WooCommerce equivalent. This protects your search engine rankings and ensures customers with bookmarked pages can still find your products. Most hosting providers make this straightforward through .htaccess rules or server-level redirect configuration.

Step 5: DNS cutover and monitoring. Point your domain to your new hosting, monitor for crawl errors in Google Search Console, and watch your server performance for the first few weeks. Have a rollback plan in case anything goes wrong. For the complete step-by-step process, see our guide on leaving Shopify without losing traffic or sales.

The bottom line

Ecommerce without Shopify is not just possible — for many stores it is the smarter business decision. When your revenue is being taxed by transaction fees, your customisation is limited by a proprietary platform, and your data is held hostage by a company that profits from making migration difficult, the case for ownership becomes impossible to ignore.

The right path depends on your situation. If you want the largest ecosystem with the lowest barrier to entry, start with self-hosted WooCommerce. If you want modern performance without giving up WooCommerce's backend, go headless. If you're a developer-heavy team building something entirely custom, explore Medusa or Saleor.

What matters is that you make the decision intentionally — not because Shopify was the first search result when you typed "how to sell online." Your store is a business asset. Own it. For more on why developers are leaving Shopify, the real cost of Shopify, and what headless WooCommerce actually costs, explore our guide library.