The verdict in three sentences
Shopify Plus puts you live in 6-10 weeks for ~2,300 EUR/month + apps + transaction fees; custom takes 4-7 months and 50,000-130,000 EUR but belongs to you. Over 3 years, both TCOs often converge: beyond a certain volume, Shopify's apps and transaction fees catch up with the custom build's upfront cost. The real question is not price but lock-in and how specific your B2B logic is.
3-year TCO (2026 order of magnitude)
| Item | Shopify Plus | Custom |
|---|---|---|
| Initial build | 15,000 - 35,000 EUR | 50,000 - 130,000 EUR |
| Platform subscription | ~2,300 EUR/mo | 0 |
| B2B apps & extensions | 200 - 1,000 EUR/mo | 0 (built in) |
| Transaction fees | 0.2 - 2 % per PSP | 0 (PSP aside) |
| Hosting | included | 200 - 700 EUR/mo |
| Maintenance | 500 - 1,200 EUR/mo | 1,000 - 2,000 EUR/mo |
| 3-year TCO (indicative) | 130,000 - 200,000 EUR | 120,000 - 210,000 EUR |
Where the curves cross depends mostly on transaction volume and the number of paid apps needed to cover your B2B requirements.
B2B features: native vs custom
| Feature | Shopify Plus (B2B) | Custom |
|---|---|---|
| Per-account / group pricing | Native | Unlimited |
| Custom catalogues | Native (limits) | Total |
| Credit & deferred payment | App / limited | Native bespoke |
| Order approval workflow | App | Native |
| Real-time ERP link | Connector | Bespoke |
| Online quotes (RFQ) | App | Native |
| Multi-currency / multi-entity | Native (limits) | Total |
Shopify Plus covers the essentials of standard B2B. Custom wins as soon as pricing logic, credit or ERP impose rules outside the SaaS model.
Switch thresholds toward custom
| Indicator | Threshold pointing to custom |
|---|---|
| Transactional revenue | > 3-5 M EUR/year (heavy transaction fees) |
| Number of paid apps | > 6 critical apps |
| Pricing logic specificity | Rules outside SaaS standard |
| ERP integration | Real-time, bidirectional |
| Reversibility requirement | High (no lock-in) |
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Mini case study
Thomas is e-commerce director of a B2B distributor in Singapore, EU subsidiary: 4.2 M EUR online revenue, 9 paid Shopify apps, complex contract pricing. On Shopify Plus, his annual TCO reaches ~62,000 EUR (subscription + apps + transaction fees + maintenance). A custom build at 95,000 EUR amortized over 3 years comes to ~48,000 EUR/year including maintenance, while removing transaction fees and lock-in. Decision to switch: estimated saving ~14,000 EUR/year from year 2, with a reversible platform.
FAQ
Is Shopify Plus really suited to B2B? Yes for standard B2B: per-account pricing, custom catalogues and customer accounts are native. Limits appear on credit, complex workflows and real-time ERP integration, often filled by paid apps.
At what volume does custom become worthwhile? As an order of magnitude, beyond 3-5 M EUR of annual transactional revenue, transaction fees and stacked apps catch up with the custom investment over 3 years. Each case is simulated with a costed TCO.
Is lock-in a real risk? Yes: on SaaS, migrating is costly and your roadmap depends on the vendor. Custom delivers the code and removes that dependency, at the price of a higher upfront investment and maintenance.
How much do Shopify B2B apps cost? Between 200 and 1,000 EUR/month depending on needs (RFQ, credit, ERP, volume discounts). This stack is often underestimated: fold it into the TCO from the start.
Can we start on Shopify then move to custom? Yes, it is a common path: validate the market on SaaS, then internalize custom when volume justifies it. Include migration cost (redirects, data) in the decision.
Let's scope your project. Share your online revenue, critical apps and B2B constraints: we will cost the 3-year TCO for Shopify Plus vs custom and recommend the best choice. 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.