Shopify vs Custom E-commerce Website: Costs, Pros and Cons, and When to Switch

Updated September 2026 with Shopify's current UK prices and fees, checked on shopify.com on 25 September 2026.

Should you sell on Shopify or build a custom online store? We build custom e-commerce sites in Django, so you might expect us to say "custom" every time. We don't. For many shops Shopify is the right answer, and a custom build only pays off when the business needs something Shopify can't do well. This guide sets out the real costs on both sides and gives you a checklist for deciding.

The short answer

• Choose Shopify if you sell standard products with simple pricing and shipping, want to launch quickly, and don't have unusual integrations. It is quick, reliable and cheap to start.
• Choose a custom build when your pricing, wholesale terms, checkout or integrations don't fit Shopify's model, or when the shop is one part of a bigger product.
• Don't switch just to save on fees. For a store with straightforward needs, card fees on Shopify and on a custom site with Stripe are close. The case for custom rests on what the store has to do.

What Shopify costs in the UK in 2026

Shopify's UK plans, as listed on its pricing page in September 2026:

The card rates apply when you use Shopify Payments. American Express and international cards cost more (3.1% + 25p on Basic), and Klarna costs 4.99% + 30p on most plans. If you use a different payment provider, you pay that provider's fees plus Shopify's transaction fee in the last column.

On top of the plan you will usually pay for:

• Apps for anything the core platform doesn't do, such as subscriptions, advanced filtering, product options, loyalty schemes or reviews. Most are monthly subscriptions, and they add up.
• A premium theme, if you don't use a free one.
• Developer time for theme changes and custom apps, because Shopify is only "no code" until you need something specific.

Some limits also depend on the plan. Below Plus, checkout customisation is limited and B2B selling is capped at 3 catalogues. Full checkout customisation, unlimited B2B catalogues and the highest API rate limits are Plus features.

What a custom store costs

A custom store has a different shape of cost: a larger upfront build, then running costs you control.

• The build, priced on scope: catalogue complexity, pricing rules, checkout, integrations and data migration. We give a detailed quote once we understand your requirements.
• Hosting, which for most stores is a modest monthly cost.
• Maintenance: security updates, monitoring, backups and small improvements. A custom store needs looking after, and you should budget for that from day one.
• Payment fees charged by your payment provider, with no platform transaction fee on top. Stripe's UK pricing in September 2026 is 1.5% + 20p for standard UK cards and 2.8% + 20p for premium UK cards, with higher rates for European and international cards.

Our guide on how to plan a custom e-commerce website covers what drives the build cost and how to scope it.

Total cost of ownership: a worked example

Here is the fee side for an illustrative store turning over £250,000 a year online, from 5,000 orders at £50 each, all paid with standard UK cards. It uses yearly plan billing and the rates above.

The honest reading: at this size, the difference in fees is a few thousand pounds a year at most, and hosting and maintenance eat into it. Fees alone will not pay for a custom build. The numbers move when:

• You use a payment provider other than Shopify Payments. On Grow, the extra 1% transaction fee on £250,000 is another £2,500 a year.
• You rely on several paid apps. Add up your real app subscriptions over three years; this is often the biggest hidden cost.
• You need Plus. From £1,800 a month, Plus costs at least £21,600 a year, or £64,800 over three years, before apps or card fees.

So a fair comparison over three years is: Shopify plan, apps, theme and developer time, plus card fees, against a custom build, hosting and maintenance, plus card fees. Put your own numbers into both columns.

When Shopify is the right choice

• You are launching or testing a product and need to start selling quickly.
• Your products, pricing and shipping rules are standard.
• You want to sell in person too: Shopify's POS is a strength.
• You don't have, and don't want, a development partner.
• Your needs are covered by a handful of well-supported apps.

There is also a middle ground. Shopify lets you build a headless storefront (a custom front end that uses Shopify for products and checkout). You get design freedom, but you keep Shopify's checkout rules and fees, and you pay for development on both sides.

When should you replace Shopify with custom software?

Run through this checklist. If several points ring true, it is worth pricing a custom build properly.

• Your pricing doesn't fit. Made-to-measure products, prices calculated from dimensions or materials, customer-specific discounts or quote-based orders that need workarounds or stacked apps.
• You sell wholesale. Trade accounts with their own price lists, minimum order quantities, credit terms, invoices or approval steps (more on this below).
• Your checkout needs to change. Extra steps, custom fields, deposits, booking dates or conditional delivery options. Full checkout customisation is a Plus feature.
• Your systems don't talk to each other. Stock, orders and customers need to sync with your warehouse, ERP or accounting software, and the apps you've tried are unreliable or hit API limits.
• The shop is part of a bigger product. Bookings, memberships, document generation or customer portals where payment is one step. UK Name Change, a deed poll platform we built with Stripe payments at its heart, is this kind of project.
• Your app bill keeps growing, and you are paying monthly for features that would be a one-off piece of work in your own code.
• SEO structure matters to you. Shopify uses fixed URL prefixes such as /products/ and /collections/, and some technical SEO changes are harder than they should be.

Shopify vs custom for wholesale businesses

Wholesale is where the gap is widest. Shopify now includes B2B tools on every plan, but below Plus you are limited to 3 catalogues (the price lists you assign to groups of trade customers), and unlimited catalogues need Plus at £1,800 a month or more. A custom build can model trade selling the way your business actually works: price lists per customer or group, volume tiers, minimum order quantities, ordering on account with credit limits, quotes that turn into orders, and a sync with the stock and accounting systems your team already uses. If most of your revenue is trade, price both routes against your real trade rules before you decide.

Why some businesses move from custom to Shopify

It happens the other way too, and the reasons are worth knowing before you commission a build:

• The custom site wasn't maintained, fell behind on security updates and became risky to change.
• The original developer disappeared and nobody else understood the code.
• The business needed Shopify's ecosystem, such as POS, marketplace syncing or a familiar admin for a growing team.

Each of these is a planning problem, not a technology problem. If you go custom, make sure you own the code and hosting accounts, the project is documented, and there is a maintenance plan in place from launch.

Shopify vs EKM, Craft Commerce and WooCommerce

EKM is a UK-based hosted platform. It is the same "rent a platform" model as Shopify, so compare the two on features, UK support and total fees rather than on ownership. Check EKM's current pricing directly, as we couldn't verify it for this update.

Craft Commerce is an e-commerce plugin for the Craft CMS, and a genuine middle ground: you host it and own the build, with strong content tools. In September 2026 a Pro licence costs $1,199 per project plus $299 a year for updates after the first year, and it needs a Craft CMS licence on top. You will need a developer to build and maintain it.

WooCommerce is a free plugin for WordPress. The software is free, but you pay for hosting, premium extensions and maintenance, and security depends on keeping WordPress and every plugin up to date.

Moving from Shopify to a custom store

If you do switch, protect what you've built:

1. Export products, customers and orders from Shopify, and decide what order history you need in the new system.
2. Map every old URL (products, collections, pages and blog posts) to its new address and set up 301 redirects before launch.
3. Keep page titles, descriptions and product copy that already rank, and add product structured data.
4. Plan a password reset email for customers, because Shopify doesn't export customer passwords.
5. Submit the new sitemap in Google Search Console and watch for crawl errors in the weeks after launch.

The verdict

Shopify is an excellent product for standard retail, and we'd recommend it to plenty of businesses. A custom store earns its cost when your business model is the thing Shopify struggles with: complex pricing, wholesale, custom checkouts, deep integrations or a store inside a larger platform. For the collectibles store Anime Weebs, for example, we built curated limited-edition drops, a streamlined inventory feed and a conversion-focused checkout into one platform.

If that sounds like your situation, find out more about our custom ecommerce website development. We're happy to tell you if Shopify would serve you better.