If you sell products and do not have an unusual requirement, start on Shopify. Checkout, payments, taxes, inventory and the security of the cart are the hardest and riskiest parts of a store, and Shopify has already built them and keeps them updated. A custom store makes sense when your selling model does not fit a standard store, and you have the budget to build and maintain it afterward. Shopify says as much in its own developer documentation: headless is for cases where themes, sales channels and apps cannot do the job, and it costs more to build and run than a theme.
What "custom store" can mean
The phrase covers three different things, and they have different costs.
- A custom Shopify theme. Shopify handles the store. A developer builds a theme designed around your products. This is the most common upgrade from a template, and it keeps Shopify's checkout and admin.
- A headless storefront on Shopify. The front of the site is custom code, and Shopify provides products, cart and checkout through its Storefront API. Shopify's own framework for this is Hydrogen. You get full control of the front end and you take on hosting and maintenance of it.
- A fully custom store. Your own database, your own cart, your own payment integrations. Or a self-hosted platform such as WooCommerce on WordPress. This gives the most freedom and the most responsibility, including security and payment compliance.
What Shopify takes off your plate
- Checkout. Hosted, tested, and kept current with payment methods.
- Payments. Shopify Payments is built in. Shopify's help center says orders using Shopify Payments carry no third-party transaction fee, while orders through a third-party payment provider add a Shopify fee that varies by plan, on top of what the provider charges. Check the current rates for your plan in your admin before you decide.
- Updates and hosting. Shopify runs the platform. You do not patch it.
- Apps. A large library covers reviews, subscriptions, bundles, loyalty and shipping. Many requests that sound custom are an app away.
What a custom Shopify theme changes
Most brands that outgrow a template do not need to leave Shopify. A developer rebuilds the theme around your products: how collections are laid out, how a product page presents sizes, materials and care, how the cart and the first screen of the homepage work. You keep Shopify's admin, so staff add products and fulfill orders the way they already do. What changes is the front of the store.
This is also where most stores gain the most with the least risk. Photography, product descriptions and page structure usually move sales more than the underlying platform. If your product pages are thin, a new architecture will not fix that. Fix the pages first, then decide whether the theme is the limit.
When a custom or headless build is worth it
- The product itself needs a tool. A configurator where customers design the product, with live pricing rules that an app cannot express.
- The brand experience is the product. An editorial-style site with heavy storytelling, motion or custom navigation, where the template layout is the limit.
- Integrations that are not off the shelf. A real-time link to your own inventory, ERP or fulfillment system.
- Several storefronts from one catalog. Different regions, brands or wholesale portals sharing data.
- Performance targets you cannot reach with a theme after sensible cleanup. Try the cleanup first, as our Core Web Vitals guide explains.
If none of these describe you, the extra cost of custom does not buy you anything customers will notice.
The upkeep question
A theme-based Shopify store needs a person to add products and run promotions. A headless or custom store needs that and a developer on call, because the front end is code that someone has to host, update and fix. Shopify tells merchants considering headless to be sure they can absorb the added expense and complexity and have developers who can maintain the storefront after launch. Ask any agency who that developer is after launch, and what happens if the relationship ends.
Leaving or moving a store
Whichever way you go, redirects decide how much search traffic survives. Shopify lets you add URL redirects in the admin (Content, Menus, URL redirects) and import them from a CSV file. Some fixed paths such as /products and /collections cannot be redirected. If you change a product handle (the end of its address), you need a redirect from the old one. Shopify also notes that redirects for a changed handle are not supported for language-specific URLs, so check that if you sell in more than one language. The redesign checklist covers the full process.
Questions to answer before you choose
- How many products and variants do you have now, and in two years?
- Does anything about the way you sell (made to order, subscriptions, wholesale, bundles) break a standard cart?
- Who adds products and runs sales every week?
- What is your tolerance for the store being down because of a bug you own?
- Do you need your own payment provider for a reason, such as a business account that requires one?
| Situation | Likely fit |
|---|---|
| First store, standard products | Shopify with a good theme |
| Standard products, strong brand and layout needs | Custom Shopify theme |
| Unusual product tool or integrations, in-house developers | Headless on Shopify |
| Entirely unusual selling model | Fully custom, with a clear maintenance plan |
Our platform guide puts Shopify next to WordPress, Webflow and custom builds for non-store sites, and Squarespace or custom covers the brochure-site version of this decision.
Want a person to look at it?
We build stores on Shopify and custom, and we will tell you if the simple option is enough. Start a quote and describe how you sell, or read how we work with ecommerce brands.
Questions people ask
Is Shopify better than a custom online store?
For most stores, yes, because checkout, payments, taxes and security are built and maintained for you. A custom store is worth it when your selling model does not fit a standard cart and you can fund ongoing maintenance.
What is headless Shopify?
A setup where the front of the site is custom code and Shopify supplies products, cart and checkout through its Storefront API. Shopify says it costs more to build and run than a theme, so it fits cases where themes, apps and sales channels fall short.
Does Shopify charge extra if I use another payment provider?
Shopify documents a third-party transaction fee that varies by plan when you use a payment provider other than Shopify Payments, on top of the provider own fees. Check the current rate for your plan in the admin.
Can I move my store off Shopify later?
Yes, but you will rebuild the design and move products, and you will need redirects for old addresses to protect search traffic. Plan this before you commit.
Written by the team at Clouds Agency, a Los Angeles creative and production consulting agency.