The verdict in three sentences
The choice is not about entry price but about 5-year TCO and how fully your B2B rules are covered. Shopify Plus / BigCommerce fit if your pricing and flows stay within the standard; custom wins as soon as pricing logic, ERP or credit limits become structural. In 2026 the real question is lock-in: what you don't control ends up costing you in workarounds.
Two cost models
| Criterion | Shopify Plus / SaaS | Custom |
|---|---|---|
| Upfront cost | 5,000 - 25,000 EUR (setup) | 60,000 - 140,000 EUR (excl. VAT) |
| Recurring cost | 2,000 - 2,500 EUR/mo + transaction | 12,000 - 25,000 EUR/yr (maint. + hosting) |
| Transaction fees | ~0.15 to 2 % per gateway | Gateway only (~1 to 1.8 %) |
| Time to launch | 6 - 12 weeks | 4 - 8 months |
| B2B customisation | Standard + apps | Total |
| Reversibility | Low (data/theme tied) | High (owned code) |
B2B specifics covered
| B2B need | Standard SaaS | Custom |
|---|---|---|
| Per-customer negotiated pricing | Partial (apps) | Native |
| Credit limits & caps | Limited | Native |
| Payment on 30/60-day terms | Via app | Native |
| Deep ERP sync | Connector | Custom |
| Buyer approval workflow | Basic | Full |
| Per-customer catalogue | Third-party app | Native |
5-year TCO
| Line item | SaaS (5 yrs) | Custom (5 yrs) |
|---|---|---|
| Setup / build | 15,000 | 100,000 |
| Subscription / maintenance | 138,000 | 90,000 |
| Apps & connectors | 24,000 | included |
| Indicative total EUR (excl. VAT) | ~177,000 | ~190,000 |
Over 5 years the two models often converge. Custom becomes more attractive at high volume or when transaction fees and apps pile up; SaaS wins when time-to-market is paramount.
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Mini case study
Sophie, digital director of a trading SME in Bordeaux (18M EUR revenue, 900 pro customers), is unsure. On SaaS she estimates 2,300 EUR/mo + 1,800 EUR/mo of B2B apps + ~1.2 % transaction on 6M EUR online, i.e. ~121,000 EUR/year. On custom, a 110,000 EUR build plus 18,000 EUR/year maintenance. From year 2, custom is cheaper and she owns her code. Decision: custom, with a V1 in 5 months.
FAQ
Is SaaS really faster? Yes for a V1: 6 to 12 weeks vs 4 to 8 months. But every non-standard B2B rule adds apps and technical debt.
When is custom clearly justified? As soon as per-customer pricing, credit limits and ERP are structural, or beyond ~5-6M EUR of annual online sales.
What does reversibility cover? With custom you own code and data. With SaaS, migrating means rebuilding themes, apps and integrations.
Can we start on SaaS then migrate? Yes, that is a valid strategy: validate the market on SaaS, then re-platform when volume justifies it.
How to compare objectively? On 5-year TCO plus a B2B functional coverage table, not on the first month's headline price.
Let's scope your project. Send us your online sales volume, pricing rules and ERP and we will build a costed 5-year TCO comparison 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.