The verdict in three sentences
Shopify Plus at around 2,000 EUR/month is unbeatable for a fast start, but its fees and B2B limits weigh in as volume grows. A custom platform at 40,000-120,000 EUR excl. VAT costs more upfront but delivers full customization and a 3-year TCO that is often lower above a certain revenue. The tipping point usually sits around 1.5 to 2.5M EUR of annual B2B sales.
Decision comparison
| Criterion | Shopify Plus | Custom |
|---|---|---|
| Entry cost | ~2,000 EUR/month | 40,000 - 120,000 EUR excl. VAT |
| Transaction fees | 0.15 to 0.6% outside Shopify Payments | 0% (excl. chosen PSP) |
| Customer pricing | Standard but limited | Unlimited, fine-grained rules |
| ERP integration | Via apps/connectors | Native, tailored |
| Launch time | 4 - 10 weeks | 4 - 8 months |
| Code ownership | No | Yes |
| Exit cost | Low | None (you own it) |
3-year TCO
Total cost of ownership often flips the intuition. Here is a 2026 estimate for a player doing 3M EUR of online B2B sales a year, excluding marketing.
| Line item | Shopify Plus (3 yrs) | Custom (3 yrs) |
|---|---|---|
| Subscription / build | 72,000 EUR | 75,000 EUR excl. VAT |
| Transaction fees (~0.3%) | 27,000 EUR | 0 EUR |
| B2B apps and connectors | 21,600 EUR | 0 EUR |
| Maintenance / evolutions | 30,000 EUR | 33,000 EUR excl. VAT |
| 3-year total (order of magnitude) | ~150,600 EUR | ~108,000 EUR |
Below 1.5M EUR in sales, Shopify Plus often wins on speed; above 2.5M EUR, custom widens the gap every year.
Mini case study
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Sophie, head of a trading SME in Lyon, does 3.2M EUR of B2B sales and already pays 2,400 EUR/month in apps and subscription on Shopify Plus, plus 0.3% fees. Over 3 years that totals about 150,000 EUR. A custom quote at 78,000 EUR excl. VAT plus 11,000 EUR/year of maintenance brings her to 111,000 EUR over 3 years, saving 39,000 EUR while finally getting the per-customer pricing rules she lacked. She picks a custom V1 in 5 months, with ROI reached in year 2.
FAQ
Does Shopify Plus really handle B2B? Yes via its B2B features (catalogs, company pricing), but with limits on approval workflows, credit terms and deep ERP integration. It is excellent for simple B2B.
At what volume does custom pay off? Order of magnitude: above 1.5 to 2.5M EUR of annual B2B sales, the savings on fees and apps cover the extra build cost.
Can we migrate from Shopify to custom later? Yes, it is a common path: start on Shopify to validate the market, then bring it in-house at 60,000-100,000 EUR excl. VAT when volume justifies it.
Who owns the data and the code? With custom, you own the code and your data with no platform lock-in. On Shopify you remain a tenant of the ecosystem.
Is custom riskier? Risk lies with the team, not the approach. With sprints shipped every 2 weeks and a scoped V1, the risk is managed like any SaaS project.
Let's scope your project. Give us your annual B2B sales volume and customization needs to compare Shopify Plus against a custom quote between 40,000 and 120,000 EUR excl. VAT. 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.