The verdict in three sentences
Over 3 years, a B2B store costs between USD 100,000 and 275,000 depending on the solution, and the initial build rarely exceeds 40% of that total. Shopify Plus is paid mostly in licence and apps, open source in maintenance and upgrades, custom in upfront investment. The right choice depends on your online volume, the complexity of your pricing and your ability to manage a vendor.
The three options and their cost lines
Take a New York wholesaler targeting USD 2,200,000 in online sales per year, 30% paid by card and 70% by ACH or wire on net-30 terms. Its needs: customer-specific pricing, order minimums, ERP integration, 1,500 SKUs.
| 3-year cost line (2026 order of magnitude) | Shopify Plus | Open source (Magento, Sylius, WooCommerce) | Custom |
|---|---|---|---|
| Platform licence | USD 82,800 (2,300 × 36 months) | USD 0 | USD 0 |
| Setup and development | USD 35,000 | USD 50,000 | USD 90,000 |
| B2B apps and extensions | USD 21,600 (600 per month) | USD 7,000 | Included |
| Hosting | Included | USD 16,200 (450 per month) | USD 12,600 (350 per month) |
| Maintenance and enhancements | USD 36,000 (1,000 per month) | USD 39,600 (1,100 per month) | USD 43,200 (1,200 per month) |
| Card processing fees | USD 52,500 | USD 52,500 | USD 39,600 (negotiated rate) |
| 3-year total | USD 227,900 | USD 165,300 | USD 185,400 |
Payment fees range from 0.15% to 2.9% depending on setup. US corporate cards often cost 2.5% to 2.9% on blended pricing, interchange-plus brings B2B Level 2 and Level 3 data down toward 2%, ACH costs well under 1% with a low cap, and Shopify adds 0.15% to 0.2% if you use a gateway other than Shopify Payments. On USD 6,600,000 collected over 3 years, each tenth of a point is worth USD 6,600.
What tips the calculation
| Situation | Cheapest option over 3 years | Why |
|---|---|---|
| Under USD 550,000 online sales per year, simple pricing | Configured open source, around USD 100,000 | No licence, little custom work |
| Small in-house team, stability needed | Shopify Plus | Hosting, security and updates managed |
| Complex customer pricing, stacked discounts | Custom | Shopify B2B apps hit limits quickly |
| Over USD 10,000,000 online sales per year | Custom or open source | Shopify Plus variable licence grows with volume |
| Heavy ERP integration (NetSuite, SAP) | Custom | Owned connector, no third-party app dependency |
| Multi-state sales tax and exemptions | Shopify Plus or custom with Avalara | Exemption certificates must be handled per buyer |
Two hidden costs show up again and again in audits. First, major version upgrades on open source: a Magento major migration costs USD 12,000 to 35,000 every 3 to 4 years. Second, app stacking on Shopify: 6 to 10 B2B apps at USD 50 to 200 a month each, with as many third-party dependencies.
How the CFO should compare quotes
Ask each vendor for a 36-month quote on the same volume assumption, split into five lines: licence, development, apps, hosting and maintenance, payment fees. Also require the exit cost: what it takes to recover customer, order and pricing data if you switch vendors. On Shopify, export is easy but app logic gets lost. On custom, check that you own the source code.
Mini case study
Marcus, CFO of a restaurant equipment distributor in New York, sells to 900 restaurants and caterers. He is weighing Shopify Plus at USD 227,900 over 3 years against a custom build at USD 185,400. Custom costs USD 55,000 more upfront, but saves USD 82,800 in licence and USD 21,600 in apps. Net 3-year gap: USD 42,500 in favour of custom. He adds one criterion: his tiered pricing by customer group and contract would require two more Shopify apps at USD 150 a month, or USD 10,800 more. The gap widens to USD 53,300, and a licence-free fourth year adds roughly another USD 35,000.
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FAQ
What does Shopify Plus really cost in 2026?
The licence starts around USD 2,300 a month on a multi-year term, then becomes variable above a certain monthly sales volume. Add USD 300 to 800 a month in B2B apps plus payment fees.
Is open source really free?
The licence is, operations are not. Hosting, security, updates and major migrations run USD 17,000 to 28,000 a year for an active B2B store.
What payment fees should a B2B store budget for?
Between 0.15% and 2.9% depending on method: ACH well under 1%, corporate cards 2% to 2.9%, international cards above 3%. Steering large baskets to ACH or wire cuts the bill sharply.
Is custom riskier?
It is when the scope is vague. With a frozen scope, source code you own and a maintenance contract, the risk gets close to that of a packaged solution.
Over what period should we compare?
At least 3 years, ideally 5 if you plan to keep the platform. Over 12 months Shopify Plus often looks cheaper, then the gap reverses.
Let's scope your project. We price your B2B store over 3 years, line by line, comparing licensed, open source and custom options, for a budget of USD 100,000 to 275,000. 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.
