The verdict in three sentences
Shopify Plus B2B wins when your pricing rules and workflow fit the standard: fast launch, predictable cost, delegated maintenance. Custom (or open source Medusa/PrestaShop) regains the edge as soon as the sales logic becomes specific and volume dilutes the upfront cost. The right call reads off the 3-year TCO, not the entry price.
The three switching thresholds
Before comparing figures, ask these three questions. They alone decide 80 % of cases.
| Threshold | Stay on SaaS if... | Switch to custom if... |
|---|---|---|
| Pricing complexity | Simple volume discounts, group grids | Crossed tiers, per-line contract rates, ERP-driven prices |
| Volume & margin | < 2M EUR GMV, thin margin | > 3M EUR GMV, upfront dilutes fast |
| Integrations | Standard connectors suffice | In-house ERP, specific PIM, WMS to sync |
If you tick a "switch" box on all three lines, custom is almost always more profitable over 3 years. A single box rarely decides the choice alone.
Comparing the three solution families
| Criterion | Shopify Plus B2B | Open source (Medusa/PrestaShop) | Full custom |
|---|---|---|---|
| Upfront cost | 5,000 - 15,000 EUR (setup) | 20,000 - 45,000 EUR net | 30,000 - 90,000 EUR net |
| Subscription / hosting | 2,000 - 2,500 EUR/month | 200 - 600 EUR/month | 100 - 300 EUR/month |
| Platform commission | Varies by plan | None | None |
| Third-party apps (B2B, ERP) | 300 - 900 EUR/month | Modules to build | Included in scope |
| Time to launch | 6 - 12 weeks | 10 - 16 weeks | 12 - 20 weeks |
| Pricing/workflow freedom | Standard | High | Total |
3-year TCO: the real arbiter
Let us project a mid-sized B2B e-commerce, excluding internal costs.
| Line item (36 months) | Shopify Plus B2B | Custom |
|---|---|---|
| Setup / build | 12,000 EUR | 55,000 EUR net |
| Platform subscription (36 months) | 81,000 EUR | 0 |
| B2B + ERP apps (500 EUR/month) | 18,000 EUR | 0 |
| Hosting (36 months) | included | 7,200 EUR |
| Maintenance (700 EUR/month) | 0 (delegated) | 25,200 EUR |
| 3-year total | 111,000 EUR | 87,400 EUR net |
At high volume and specificity, custom drops below SaaS from year 3. Conversely, for a fast launch or standard scope, Shopify Plus limits upfront risk and shortens the timeline.
Mini case study
Need a professional website?
Kolonell builds websites that attract clients, optimized for the Sénégalese market. Free quote in 2 minutes.
Sophie, head of a building-materials trader in Amsterdam, is hesitating. She has 2,400 SKUs, per-project contract pricing and an in-house ERP. On Shopify Plus, the 3-year TCO comes to ~118,000 EUR with two B2B apps and a fragile ERP connector. In custom (build 58,000 EUR net, maintenance 750 EUR/month, hosting 200 EUR/month), her 3-year TCO drops to ~92,000 EUR net, a 26,000 EUR saving and, above all, total freedom over her per-project pricing. Verdict: custom, justified by pricing complexity and the ERP.
FAQ
At what volume does custom become profitable?
As an order of magnitude, above 2.5 - 3M EUR annual GMV, the upfront cost dilutes and the 3-year TCO often tips toward custom. Below that, SaaS stays safer.
What does Shopify Plus B2B really cost in 2026?
Expect 2,000 - 2,500 EUR/month platform, plus 300 - 900 EUR/month of B2B apps and connectors, excluding initial setup (5,000 - 15,000 EUR).
Is open source a good compromise?
Yes for technical teams: Medusa or PrestaShop offer high freedom at 20,000 - 45,000 EUR net build, with no commission or heavy subscription, but with maintenance to own.
Is timeline a decisive factor?
Often yes: if you must launch within 3 months, Shopify Plus (6 - 12 weeks) beats custom (12 - 20 weeks). A hard deadline sometimes justifies starting on SaaS then migrating.
Can I migrate from Shopify to custom later?
Yes, a common scenario: validate the market on SaaS, then internalise when volume and specificity justify it. Plan a clean catalogue/customer export.
Let's scope your project. Send us your annual volume, pricing rules and ERP: we compute your 3-year TCO SaaS vs custom and recommend the right scenario (build 30,000 - 90,000 EUR net). 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.
