The verdict in three sentences
Shopify Plus starts at 2,000 USD/month plus per-transaction fees if you skip Shopify Payments, and launches fast but constrains your B2B specifics. Custom costs 40,000 to 115,000 USD to build, with no platform subscription, native regional payment rails and zero commission. The right choice depends on your volume, the specificity of your B2B rules and your 3-year horizon.
Direct comparison 2026
| Criterion | Shopify Plus | Custom |
|---|---|---|
| Launch cost | 5,000 - 20,000 USD | 40,000 - 115,000 USD |
| Monthly platform cost | ~2,000 USD + | 0 (hosting 250-1,000) |
| Transaction fee | 0.15-0.6 % off Shopify Pay | 0 % |
| Native local payment rails | via third-party app | native |
| Complex B2B rules | limited | unlimited |
| Lock-in / portability | high | you own the code |
| Time-to-market | 4 - 8 weeks | 12 - 24 weeks |
Shopify Plus wins on speed; custom wins once your business rules or commission costs get heavy.
The tipping point: 3-year total cost
The subscription trap runs continuously. Over 36 months the math often flips.
| Line over 3 years | Shopify Plus | Custom |
|---|---|---|
| Platform subscription | ~72,000 USD | 0 |
| Commissions (on 5M USD sales) | 7,500 - 30,000 USD | 0 |
| Paid apps (B2B, pricing) | 10,000 - 25,000 USD | included |
| Initial build | 10,000 USD | 75,000 USD |
| Hosting / maintenance | included | 20,000 - 34,000 USD |
| Total order of magnitude | 100,000 - 137,000 USD | 95,000 - 109,000 USD |
Under about 800,000 USD annual sales and without heavy B2B rules, Shopify Plus stays unbeatable. Beyond that, or with specific B2B and local rails at the core, custom becomes cheaper and more flexible.
Mini case study
Amira, GM of a food distributor in Dubai (3M USD e-commerce sales, high share of local wallet payments), compares both. On Shopify Plus, her commissions and B2B apps reach 35,000 USD/year, or 105,000 USD over 3 years. A custom build at 80,000 USD + 9,000 USD/year hosting comes to 107,000 USD over 3 years but removes lock-in and integrates local rails natively, saving 1.4 % of recurring commission. At her volume, custom is profitable from year 2.
FAQ
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Does Shopify Plus really handle B2B?
It offers a B2B module (company pricing, accounts), but complex rules (quotas, credit, nested grids) quickly hit limits needing apps or code, with a rising monthly cost.
Do local wallets work on Shopify?
Via third-party apps, with fees and dependence on the app vendor. In custom, the integration is native, with no app commission or intermediary.
What volume justifies custom?
As a 2026 order of magnitude, beyond 800,000 to 1.3M USD annual sales or with specific B2B rules, custom TCO becomes competitive over 3 years.
Is lock-in a real risk?
Yes: migrating off Shopify is costly and your customer/order data lives in their ecosystem. With custom, you own the code and database.
Can we start on Shopify then migrate?
A common strategy: validate the market on Shopify, then migrate to custom at the tipping point. Budget 25,000 to 65,000 USD for migration depending on catalog.
Let's scope your project. Give us your annual e-commerce sales, your local-payment share and your B2B rules: we will size the 3-year TCO comparison, indicative custom budget 40,000-115,000 USD. 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.
