Shopify vs Custom B2B Store: The Decision in Amsterdam (2026)

The verdict in three sentences

Shopify wins on speed and start-up cost; custom wins on control, B2B rules and TCO at high volume. For an Amsterdam director, the real question is not the sticker price but the total cost over 3 years: subscription + apps + transaction cuts vs a one-off investment. Custom becomes cost-effective once your business specifics or your volume make the stack of apps and cuts pricier than the build.

The real comparison: 3-year TCO

Shopify charges a monthly subscription, apps and, outside Shopify Payments, up to 2 % per transaction. Custom is a one-off investment plus hosting. 2026 order of magnitude for a mid-volume store:

At low volume, Shopify is unbeatable. The maths flips when apps multiply and the 2 % cut weighs on high revenue.

When custom wins: the switch-over thresholds

Four criteria tip the balance toward custom; two or more, and the decision leans.

Shopify's hidden risk is lock-in: migrating later costs €25k-€60k — so decide early if your trajectory demands it.

Mini case study

Elise runs a professional-equipment retailer in Amsterdam: €620,000 online revenue, €210 average basket, half consumer, half trade. On Shopify she stacks €349/month subscription, €280/month of apps (B2B, quoting, ERP, loyalty) and a 2 % cut because she uses a third-party PSP — about €19,900 a year. She moves to a custom store at €48,000 with trade accounts, credit limits and native ERP connection. From year 2, her annual cost drops to about €3,600 (hosting + light maintenance). Over 3 years she saves nearly €30,000 while gaining full control of the checkout and her B2B rules. Payback on the build: about 20 months.

FAQ

Is Shopify really more expensive in the long run? Not always: at low volume and without costly apps, Shopify stays the best choice. It gets expensive when apps multiply and the 2 % cut applies to high revenue — that is where custom catches up and overtakes.

Can I avoid Shopify's 2 % cut? Yes by using Shopify Payments, but you lose free choice of PSP and its negotiated rates. With a third-party PSP, Shopify adds up to 2 % on top of PSP fees — hence the weight on large volumes.

How long for a custom store? Budget 3 to 5 months depending on scope: 3 months for a polished catalogue and B2C checkout, 5 months with trade accounts, credit limits, quoting and real-time ERP connection.

Is custom riskier than Shopify? The risk lies in the vendor's quality, not the approach: clean, documented, tested code is as reliable as Shopify, without the lock-in. Demand code ownership, tests and a maintenance plan.

How do I migrate without losing SEO? Through an exhaustive 301 redirect plan, keeping key URLs and an SEO QA before switch-over. Done well, a migration preserves traffic; botched, it can cost 20-40 % of visibility for months.

Let's scope your project. Share your online revenue, current apps and B2B needs, and we will compute your Shopify vs custom TCO over 3 years and recommend whether to switch. Detailed quote within 48 h. WhatsApp +221 77 596 93 33.