The verdict in three sentences
For B2B e-commerce in 2026, Shopify Plus offers unbeatable time-to-market (2 to 4 months) but bills ~24,000 EUR/year plus apps and a paid ERP integration. A custom platform demands ~80,000 EUR to build then ~1,000 EUR/month, but absorbs your quotes, credit limits and ERP connections without limit. The tipping point appears around 90,000-110,000 EUR of cumulative cost, usually by year three.
The criteria that tip the balance
The make-or-buy debate turns on three axes: B2B specificity (quotes, credit limits, contracts), time-to-market and vendor dependency. Shopify Plus excels when your rules are standard; custom wins when each customer has its own grid and the ERP drives everything.
| Criterion | Shopify Plus | Custom |
|---|---|---|
| Online quotes and negotiation | Via apps (limited) | Native, unlimited |
| Credit limits and balances | Partial | Complete |
| Deep ERP integration | Paid connectors | Owned custom |
| Time-to-market | 2 - 4 months | 4 - 9 months |
| Vendor lock-in | High | Low (code delivered) |
| Complex rule scalability | Capped | Unlimited |
3-year TCO and tipping point
Total cost of ownership (TCO) separates the two options better than list price. Here is a 2026 order of magnitude for a mid-sized B2B e-commerce.
| Line item (over 3 years) | Shopify Plus | Custom |
|---|---|---|
| Initial build / integration | 30,000 EUR | 80,000 EUR |
| Platform subscription | 72,000 EUR (2,000/mo) | 0 EUR |
| Third-party apps (B2B, ERP) | 18,000 EUR | 0 EUR |
| Hosting + maintenance | included / 6,000 EUR | 36,000 EUR (1,000/mo) |
| Enhancements | 12,000 EUR | 15,000 EUR |
| 3-year TCO | ~132,000 EUR | ~131,000 EUR |
At this profile, both options converge near 130,000 EUR over 3 years: Shopify wins on speed, custom wins from year 4 (no subscription) and on autonomy. Below 3,000 orders/month, stay on Shopify; above that, custom widens the gap.
Mini case study
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Nadia, sales director at a medical equipment distributor in Lyon, is torn. Her catalog has 6,800 SKUs with prices per hospital and 60-day credit terms. On Shopify Plus, B2B pricing apps handle only 3 discount tiers: not enough.
She quotes a custom build at 86,000 EUR + 1,000 EUR/month. By moving quoting online (today 40 quotes/day handled manually at 12 min each), she frees 8 hours/day, about 1,760 hours/year at 35 EUR/h = ~61,600 EUR/year. The custom build pays back in ~17 months, and the 3-tier discount limit disappears.
FAQ
Does Shopify Plus really handle B2B? Yes, via B2B on Shopify (companies, per-customer catalogs and prices), but very complex cases (framework contracts, multi-criteria discounts) need apps or code, which erodes the price advantage.
When does custom become profitable? Usually from year 3-4, once the Shopify subscription (~24,000 EUR/year) accumulates. The larger your volume and rules, the sooner the threshold arrives.
Does time-to-market justify Shopify? Often yes to validate a market: 2 to 4 months versus 4 to 9. Many start on Shopify then migrate to custom once the model is proven.
How do we avoid vendor lock-in? Custom delivers source code; on Shopify, plan an exit strategy and regular data exports to limit lock-in.
What is the real hidden cost of Shopify Plus? Third-party apps: budget 300 to 800 EUR/month combined for B2B pricing, an ERP connector and advanced features, i.e. 10,000 to 30,000 EUR over 3 years.
Let's scope your project. Send us your monthly volume, pricing-grid complexity and ERP, and we'll produce a costed 3-year TCO comparison of Shopify vs custom. 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.