The short answer
For most stores selling physical products to consumers, Shopify is the right answer and a custom build is an expensive way to arrive at the same place slower. A custom or headless build only earns its cost when your catalogue, your pricing rules or your integrations do something a hosted platform genuinely cannot.
That is roughly nine stores in ten. This article is about working out whether you are the tenth, because the honest comparison has three options in it, not two.
The three real options
The differences show up in who does the work when something breaks.
Shopify
A hosted platform. Shopify runs the servers, the checkout, the payment security and the updates. You pay a monthly subscription, pick a theme, install apps for the gaps and start selling. The checkout is the strongest part of the product. It is tested against enormous volume and you are not allowed to break it, which is a feature disguised as a restriction.
The constraint is that you live inside their model of a shop. Products, variants, collections and discounts behave as Shopify decided, and when you need something different you reach for an app, then another, and the monthly cost creeps.
WooCommerce
A plugin that turns WordPress into a shop. You own the code and the database, hosting is yours to choose, and there is a plugin for almost everything. It suits businesses already running a large WordPress content site, or with unusual tax, membership or booking rules an existing plugin handles.
The cost is ownership. Updates, security patches, plugin conflicts, performance tuning and backups are your problem or your agency's. A store carrying twenty plugins is a maintenance commitment, not a one time build.
A custom or headless build
A shop built as an application, usually with a React or Next.js front end and either a headless commerce engine or your own backend behind it. Everything is possible and everything must be written. This is what we build in our web development work when a store is a product with a checkout attached.
Shopify vs WooCommerce vs custom, side by side
| Factor | Shopify | WooCommerce | Custom or headless |
|---|---|---|---|
| Typical build cost | From $4,500 | $4,000 to $12,000 | $18,000 upwards |
| Time to launch | 2 to 5 weeks | 4 to 8 weeks | 10 to 20 weeks |
| Monthly platform cost | Subscription, rising with plan tier | Hosting only, modest to significant | Hosting plus any engine licence |
| Apps and plugins | Often the largest hidden monthly line | Many free, paid ones add up | Written, not bought |
| Transaction fees | Extra percentage unless you use their payments | Only your gateway rate | Only your gateway rate |
| Flexibility | High inside their model, low outside it | Moderate, limited by plugin quality | Total, at the cost of building it |
| Maintenance burden | Handled for you | Yours every month | Yours, but no plugin conflicts |
| Who it suits | Most product stores under a few thousand SKUs | Content led sites that also sell | Complex catalogues, B2B pricing, deep integrations |
Two rows decide most projects. The transaction fee row is the one people underestimate, and the flexibility row is the one people overestimate that they need.
What platform fees actually do to your margin
Shopify charges a subscription, plus an extra percentage on each sale if you process payments through a third party gateway rather than their own. Use their payments and that surcharge goes away, though your gateway rate still applies. Rates change and vary by country, so check current figures for your market rather than trusting a number in any article, this one included.
Then run the arithmetic too few founders do. Work out your total platform cost as a percentage of revenue now, and at three times your current volume. Under about one per cent, the argument for building your own is weak. Climbing towards three per cent in a slim margin category, a custom build starts paying for itself.
Apps are the other quiet cost. A store running subscriptions, bundles, reviews, loyalty, search and a page builder can pay more each month for apps than for the platform.
Where Shopify stops being enough
We recommend moving off a hosted platform when a store hits one of these, not before:
- Catalogue complexity. Configurable products with dependent options, made to order items, or SKUs priced by dimension, weight or material. Variant limits are where hosted platforms bend first.
- Customer specific pricing. B2B accounts with negotiated price lists, credit terms, approval workflows or per customer catalogues. Some of it is possible with the right apps, and all of it is fragile.
- Deep integration. Live stock and pricing from an ERP, a warehouse system that must confirm before checkout, or a quoting engine that sets the price. Once business logic sits between basket and order, workarounds cost more than a build would have.
- Scale economics. Enough revenue that platform percentages exceed what engineering would cost.
None of those are "we want a unique design". Shopify themes can be customised heavily, and a distinctive storefront is not a reason to leave. We do that inside our Shopify development service, where stores start at $4,500 with a custom theme rather than a generic install.
What a custom build really costs to own
The build price is the smaller half. A custom store also carries everything the platform used to do for you.
- Payments, fraud checks and compliance work that Shopify absorbs into its subscription.
- Hosting, monitoring, backups and an on call answer to who fixes checkout at 2am.
- Every feature you would otherwise install in an afternoon: reviews, wishlists, abandoned basket emails, tax rules per market.
- Ongoing development, because a custom platform without a maintenance budget becomes legacy in about eighteen months.
Budget from $18,000 for a serious custom or headless store, and fifteen to twenty per cent of that annually to keep it healthy. Our published prices start web apps at $12,000 for a reason: a shop with real business logic is an application, and pricing it like a website is how projects go wrong.
How to decide in ten minutes
Answer these honestly and the platform usually picks itself.
- How many products, and do any need options that depend on other options?
- Do different customers see different prices?
- Does another system hold the truth about stock, price or availability?
- What would platform costs be as a percentage of revenue at three times your volume?
- Who maintains this in a year, and is that person paid to?
- How soon do you need to be selling?
If the answers are "a few hundred simple products, one price for everyone, no external system, under one per cent, nobody in house, as soon as possible", open a Shopify account. If two or more point at complexity, get both routes quoted first. Across the builds on our work page the pattern holds: successful custom stores all had a specific reason, and it was never aesthetics.
Whatever you choose, the platform is not what makes a store sell. Photography, page speed, delivery promises and traffic do, which is what a serious paid and organic acquisition plan buys you.
Frequently asked questions
Is Shopify better than a custom ecommerce website?
For most stores, yes, because it handles checkout, security, hosting and payment compliance for a predictable fee. A custom build is better only when your catalogue, pricing rules or integrations do something Shopify cannot, and that threshold is higher than most founders assume. Start hosted, move when a requirement forces it.
Shopify vs WooCommerce: which should a small business choose?
Choose Shopify if selling is the main job of the site and you do not want to maintain software. Choose WooCommerce if you already run a substantial WordPress content site, or need a plugin that exists nowhere else. WooCommerce is cheaper on paper and more expensive in attention.
When is a custom ecommerce build worth the money?
When platform fees at your revenue exceed the cost of engineering, or a core requirement cannot be met without stacking fragile workarounds. Typical triggers are B2B pricing, configurable made to order products and live ERP integration. Model the three year total for both routes before committing.
Can I migrate from Shopify to a custom store later?
Yes, and planning for it costs almost nothing today. Keep your product data clean and exportable, avoid apps that hold data you cannot get back, and keep your URLs sensible. Migration is mostly data mapping and redirects, both easier when the original store was tidy.
How much does a Shopify store cost to build?
A custom themed store built properly usually starts around $4,500 and rises with catalogue size, integrations and the number of templates. On top of that sit the subscription, payment processing and apps, which together often cost more per month than founders budget for. Cheaper builds exist, and they are usually a stock theme with your logo on it.
If you are stuck between the two, send us your product count, your pricing rules and any system that has to talk to the store. We will tell you which route we would choose and give you a fixed quote for it, including the monthly running cost.
Next step
Want this working in your business?
A 30-minute call is enough for us to tell you what would move the needle first, what it costs and how long it takes.
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