Why Growing Webshops Are Leaving Shopify

Shopify charges transaction fees of 0.5% to 2% on every sale if you do not use their own Shopify Payments. That sounds small when you see it as a percentage. But run the numbers to real amounts: at €200,000 revenue per year, that is €1,000 to €4,000 you pay on top of your payment provider's transaction costs. At €500,000 revenue, it climbs to €2,500 to €10,000 per year. At €1 million, you pay €5,000 to €20,000 in Shopify's platform percentage alone.

This is the fundamental problem with Shopify's revenue model: the more successful you become, the more you pay. Not for more functionality. Not for better service. Not for extra features. Simply because you sell more. It is a tax on growth that weighs heavier the better your business does. At €200,000 revenue, that is up to €4,000 per year. Do you know what you could do with €4,000? Run a complete Google Ads campaign. Pay half an employee for a month. Get your product photography done professionally. Instead, it quietly disappears to Shopify, every single month.

And it does not stop at transaction fees. Shopify Payments is only available in certain countries and forces you into their terms and their payment methods. Want to use a different payment provider that fits the Dutch market better (like Mollie, with iDEAL, Bancontact and all the other methods your customers expect)? Then you pay the extra percentage. You are penalised for choosing a payment solution that is better for your customers.

The irony is painful: the businesses that pay the most to Shopify are exactly the businesses that need the least of what Shopify offers. They have the scale, the knowledge and the budget to stand on their own feet. Yet they pay more every month because switching seems complicated. That "complicated" costs them thousands of euros per year.

Count your Shopify apps. Eight? Ten? Each one costs you money, slows your site down, and could break tomorrow after an update. An average Shopify webshop uses 6 to 12 apps to provide functionality that Shopify does not have out of the box. Each app solves a specific problem: advanced filters for your product catalogue, bundle deals, loyalty programmes, upsell popups, automated emails, translation capabilities, advanced analytics, SEO tools, review systems, back-in-stock notifications.

Each app costs €10 to €100 per month. Some premium apps cost more. With 8 apps, you are quickly at €200-€500 per month in app costs alone. That is €2,400 to €6,000 per year, on top of your Shopify subscription and your transaction fees. Over three years, that is €7,200 to €18,000 on functionality that would have been standard with a custom platform.

But the financial cost is not even the worst part. The real problem is technical. Every app adds JavaScript to your website. Every app makes API calls that slow your page down. Every app is a separate piece of software independently maintained by a different developer or company. Apps conflict with each other, cause unexpected bugs after updates, and sometimes break when Shopify updates their platform.

The result: a webshop that started out fast and clean gradually becomes a patchwork of third-party code. Your page loads in 4-5 seconds instead of 2. Your mobile score on Google PageSpeed drops to 30-50 out of 100. And every extra second of load time costs you 7% conversion. At 10,000 visitors per month, the difference between a page that loads in 2 seconds and one that needs 4 seconds is: 28 missed orders per month.

This is not a hypothetical scenario. This is the reality of virtually every Shopify shop that has been running for more than a year and uses more than a handful of apps. It starts small, grows gradually, and by the time you notice, you are stuck in an ecosystem of dependencies that is hard to untangle.

Try building a product calculator in Shopify. Or a custom checkout for B2B customers. Or dynamic shipping costs based on weight. That is where the freedom stops. Shopify's theme editor gives you the feeling that you can customise everything. Change colours, pick fonts, rearrange sections, upload a logo. That feels like freedom. But try to do something that falls outside the theme. A custom product calculator that computes tiles per square metre. A unique checkout flow with extra steps for B2B customers. A dynamic pricing table that changes based on quantity and size. Then you hit a wall.

Shopify's checkout is largely locked on all plans except Shopify Plus. You can make limited styling adjustments (colours, fonts), but the structure and logic belong to Shopify. Want to add a step for gift wrapping? A field for a purchase order number for B2B customers? A calculation that dynamically adjusts shipping costs based on weight and destination? Then you need Shopify Plus (starting at €2,300 per month) or an expensive workaround via an app that tries to hack around it.

For DTC brands that want to differentiate through their customer experience, this is a serious limitation. Your brand experience ends where Shopify's template begins. Every Shopify checkout looks the same, feels the same, works the same. Your customer leaves your carefully crafted brand world and lands in a generic checkout identical to thousands of other shops.

With a custom webshop, you design the checkout as part of your brand experience. Every step, every field, every confirmation page is yours. The checkout feels like a seamless part of your brand, not a generic form you rent from Shopify. That is the difference between a brand that rents a platform and a brand that owns and controls its own experience.

Your customer data is the most valuable asset of your webshop. But with Shopify, it is not yours. Your customer data, order history, product data and analytics sit on Shopify's servers. You can export them as CSV files, but real-time access to your data goes through Shopify's API. That API has limits: a maximum number of requests per second, restrictions on which data you can query, and rules Shopify can change unilaterally.

What does that mean concretely for your daily operations? You cannot query your own data without limits for analyses. You cannot build custom dashboards that show your data in real time without hitting API limits. You cannot run advanced customer analyses on your full order history. And when Shopify decides to change a feature, restrict an API, or remove a data field, you have no choice but to adapt.

This is not a theoretical risk about something that might possibly happen someday. In 2023, Shopify raised their prices by 33% for all plans, overnight. Merchants who had been loyal for years and paid thousands of euros per month were given one month to accept or leave. Leaving means rebuilding your entire webshop: your theme, your app configurations, your checkout adjustments, everything. You can take your data, but not your webshop.

That is the reality of platform dependency. You always have less bargaining power than the platform. They set the rules, the prices and the terms. You can accept or leave, and leaving gets more expensive the longer you stay on the platform.

For growing businesses, data is the most valuable asset after the team. Customer behaviour, purchase patterns, seasonal effects, product performance, conversion patterns. Those insights are the foundation for better decisions about purchasing, marketing, product range and pricing. If that data is locked inside a platform you do not control, with API limits you do not determine, you are limiting your own ability to grow data-driven.

A custom webshop does not mean you have to build, host or maintain everything yourself. It means you have a platform specifically built for your business, on servers you control, with data that is yours, and with functionality that fits your workflow instead of a generic template.

Concretely, switching from Shopify to custom means the following:

Your products, customers and order history are fully migrated to your own system. Nothing is lost. Your customers only notice that the webshop looks better and works faster.

You pay through Mollie only direct transaction costs (€0.29 per iDEAL payment, 1.8% + €0.25 per credit card payment). No platform percentage on top. Every euro Shopify was taking as a platform fee now stays in your business. At €200,000 revenue, that is up to €4,000 per year back in your pocket. Over three years, that is €12,000 you can invest in growth instead of giving away to a platform.

Functionality you currently handle through 8 or more apps is built into your platform as a native component. No monthly app costs, no extra scripts slowing down your site, no conflicts between apps after updates.

You get a client portal where you manage everything: add and edit products, process and invoice orders, view analytics, edit content via a visual CMS. Just as user-friendly as Shopify's backend, but tailored to your specific way of working.

Your data is fully yours, without limitations. No API limits, no platform dependency. You can run custom analyses, build integrations with your accounting software or CRM, and leverage your customer base for targeted marketing without restrictions from a third party.

The investment: under five figures one-time for the build, a fixed monthly fee for hosting, maintenance and portal access. Compare that with your current monthly Shopify invoice (subscription + apps + transaction fees) and the maths makes itself.

Not every Shopify shop needs to switch, and not every moment is the right moment. If you are just starting, under €50,000 revenue per year and happy with the standard functionality, Shopify is fine. It does what it needs to do and lets you focus on selling instead of technology. The switching moment is when Shopify's invisible costs start holding back your growth instead of supporting it.

Three signals that it is time for a serious conversation about custom:

1. Your app costs are higher than €200 per month. That is €2,400 per year on functionality that would be built into a custom platform as standard. And the amount only grows as you want more from your webshop.
2. Your transaction costs are noticeable in your P&L. At €150,000+ revenue, you pay €750 to €3,000 per year in Shopify's platform percentage alone. That is money going to Shopify in exchange for nothing extra. No extra features, no better service, no higher quality. Just because you sell more.
3. You are hitting limitations that concretely hold back your growth. A product calculator you cannot build within Shopify's constraints. A supplier integration that no app can deliver the way your business needs. A checkout that does not fit your brand or customer type. Reporting you cannot generate because of API limits.

The best moment to switch is not when you are frustrated and cannot take it anymore. It is when you are planning the next growth phase and consciously choosing the foundation that supports that growth. A platform migration is easiest and least risky when you choose it deliberately and take the time to do it properly, not when circumstances force you into it and you have to scramble.

Ready to do the maths? We will look at your current Shopify costs and show you what the alternative delivers. No strings attached.