The verdict in three sentences
In 2026, Shopify Plus is still unbeatable for launching a standard B2B store fast, but its commissions and stacked apps inflate cost as you scale. A custom platform costs more to build (50,000 to 180,000 EUR) but delivers total fit, zero commission and no app-store dependency. The tipping point comes down to one figure: your annual GMV and the complexity of your B2B rules.
3-year TCO: the two models head to head
Total cost of ownership matters more than the sticker price. Here is a 2026 order of magnitude for a mid-catalog B2B (5,000 SKUs, per-customer pricing, ERP integration).
| Item (3 years) | Shopify Plus | Custom |
|---|---|---|
| License / subscription | ~83,000 EUR (2,300 EUR/mo) | 0 EUR |
| Initial build | 15,000-40,000 EUR (theme + setup) | 50,000-180,000 EUR |
| B2B apps (pricing, ERP, portal) | 12,000-30,000 EUR | included |
| Platform commission | 0.15-0.25% of GMV | 0 EUR |
| Hosting / infra | included | 6,000-18,000 EUR |
| Maintenance / evolutions | 20,000-45,000 EUR | 25,000-60,000 EUR |
| Indicative TCO | 130,000-230,000 EUR | 90,000-260,000 EUR |
Below ~3M EUR annual GMV, Shopify Plus is often cheaper. Beyond that, commissions and subscriptions tilt the balance toward custom.
What custom actually unlocks
The real B2B issue is not price but functional depth: per-customer pricing rules, credit limits, approval workflows, account-restricted catalogs.
| B2B need | Shopify Plus | Custom |
|---|---|---|
| Negotiated per-customer pricing | via apps | native, unlimited |
| Quick order / reorder | via apps | native |
| Credit / net-terms payment | limited | complete |
| Real-time ERP sync | connector | bespoke |
| Order rules (MOQ, multiples) | partial | total |
| Vendor lock-in | high | none |
| Break-even (GMV/year) | < 3M EUR | > 3M EUR |
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Mini case study
Thomas, e-commerce director of an industrial distributor in Nantes, runs 6M EUR of online GMV. On Shopify Plus he pays 27,600 EUR/year in subscription, 9,000 EUR/year in B2B apps and roughly 12,000 EUR/year in commissions (0.2%), i.e. 48,600 EUR/year. A custom platform at 130,000 EUR amortized over 4 years with 35,000 EUR/year maintenance costs 67,500 EUR in year one, then 35,000 EUR/year. From year 2 he saves over 13,000 EUR/year while removing app limits.
FAQ
When should you stay on Shopify Plus in 2026? If your GMV is below 3M EUR/year and your B2B rules are standard, the 2,300 EUR/month subscription is the best speed-to-cost ratio. You go live in 6-10 weeks.
Does custom really eliminate commissions? Yes. You only pay your PSP fees (1-2.5%), no platform commission on GMV, which is 10,000-30,000 EUR/year saved beyond 5M EUR of GMV.
How long to build a custom platform? Expect 4 to 8 months depending on catalog and ERP integrations, versus 6-10 weeks for a Shopify Plus setup. Time is the real hidden cost of custom.
Can we migrate from Shopify Plus to custom later? Yes, and it is a common path: validate the market on Shopify, then move to custom when scaling. Budget 8,000-40,000 EUR for the migration.
What is the main risk of custom? Dependence on your vendor and technical debt if the code is poorly documented. Insist on delivered, documented code and a team able to take over.
Let's scope your project. Give us your GMV, SKU count and ERP integrations, and we will price the Shopify Plus vs custom tipping point for your case. Detailed quote within 48 h. WhatsApp +221 77 596 93 33.
Mohamed Bah
Fondateur, Kolonell
Passionate about digital and entrepreneurship in Africa, Mohamed has been helping Sénégalese businesses with their digital transformation since 2020. Founder of Kolonell, he believes every SME deserves a professional and accessible online présence.
