The verdict in three sentences
Licensed SaaS (Shopify Plus, BigCommerce, Commercetools) secures a 3-month time-to-market but locks you into an annual licence that climbs with your revenue. A custom headless stack demands 60,000 to 180,000 EUR up front and 6 months, but makes you the owner and collapses recurring cost. Over three years the TCO comes down to under 15% difference: the real question is not price, it is the control you want over your B2B rules.
The two cost models, priced for 2026
A B2B site is not a consumer store: you need customer accounts, contract-negotiated pricing, recurring orders, approval workflows and an ERP link. These needs shift the cost curve.
| Item (2026 order of magnitude) | Licensed SaaS | Custom headless |
|---|---|---|
| Licence / year | 24,000 – 120,000 EUR | 0 EUR (infra ~6,000 – 15,000 EUR/yr) |
| Initial integration | 25,000 – 70,000 EUR | 60,000 – 180,000 EUR |
| Time-to-market | 3 months | 6 months |
| B2B rule customization | Limited (apps/API) | Total |
| Vendor lock-in | High | None |
| Maintenance / year | 12,000 – 30,000 EUR | 18,000 – 40,000 EUR |
SaaS wins on speed and managed infra; custom wins on functional freedom and no licence indexed to your sales.
3-year TCO: the real decision ground
Comparing an annual licence to a one-shot is misleading until you cumulate. On a B2B site processing 8M EUR of volume, here is the estimate.
| 3-year cumulative (estimate) | Licensed SaaS | Custom headless |
|---|---|---|
| Licences (3 × 60,000) | 180,000 EUR | 0 EUR |
| Hosting infra | 9,000 EUR | 33,000 EUR |
| Initial build | 45,000 EUR | 120,000 EUR |
| Maintenance (3 yrs) | 66,000 EUR | 90,000 EUR |
| 3-year total | 300,000 EUR | 243,000 EUR |
Beyond three years the gap widens in favour of custom because the licence keeps running. Under an 18-month horizon, SaaS almost always stays more profitable.
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Mini case study
Thomas, e-commerce director of an electrical supplies distributor in London (7,000 SKUs, 1,200 trade accounts), is torn. SaaS promises a 12-week go-live, but his pricing rule — tiered discount AND framework contract — does not fit the standard engine without two apps at 900 EUR/month. In custom, that rule is native. He projects a 640 EUR average order and 90 orders/day: at +6% conversion from a custom B2B checkout, that is 1.04M EUR of additional volume/year, paying back the 120,000 EUR build in under 5 months of margin. He picks headless.
FAQ
Is licensed SaaS always cheaper at the start? Yes: budget 25,000 to 70,000 EUR of integration versus 60,000 to 180,000 EUR custom. The initial gap can be 2 to 3 times, but it erases over three years because of licences.
Can you customize SaaS for complex B2B rules? Partially. Per-customer pricing, quotes, quotas: most go through apps (500 to 1,500 EUR/month) or the API, with limits. Truly atypical cases stay blocked.
How long to go live? 3 months on a well-scoped SaaS, 6 months on custom headless including ERP integration. A headless MVP can ship in 4 months with a tight scope.
What about vendor dependence? High on SaaS: licence hikes, app deprecation, imposed roadmap. None on custom, at the cost of a maintenance team you must budget (18,000 to 40,000 EUR/year).
At what volume does custom become obvious? Above roughly 6 to 8M EUR of processed volume and a 3-year horizon, custom generally moves ahead, especially if your B2B rules break the standards.
Let's scope your project. Tell us your processed volume, your B2B pricing rules and your horizon: we price SaaS and custom side by side with a 3-year TCO. 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.