The verdict in three sentences
Over 3 years, Shopify Plus totals $160,000 to $205,000 all-in for a B2B manufacturer stacking apps, versus $118,000 to $172,000 for a mid-range custom store. Shopify Plus wins when your catalogue is simple and you also sell to consumers. Custom wins once you manage customer-specific price tiers, negotiated quotes and ordering rules specific to your pharmacy network.
The real cost of Shopify Plus for a B2B manufacturer
The subscription is only the visible part. A cosmetics manufacturer selling to pharmacies needs B2B apps, an ERP connector and an agency for the theme. 2026 orders of magnitude, at $1 = EUR 0.93.
| Shopify Plus item | Monthly cost | 3-year cost |
|---|---|---|
| Plus subscription (3-year term) | $2,300 (EUR 2,140) | EUR 77,000 |
| B2B apps (quotes, tiers, minimum order) | EUR 400 to 900 | EUR 14,000 to 32,000 |
| ERP connector (Celigo, middleware) | EUR 300 to 700 | EUR 11,000 to 25,000 |
| Initial agency setup | Fixed fee | EUR 25,000 to 45,000 |
| Theme maintenance and changes | EUR 500 to 1,000 | EUR 18,000 to 36,000 |
| Payment fees outside Shopify Payments | 0.15 to 0.3% of revenue | Variable |
| Estimated total | EUR 145,000 to 215,000 |
The weak point is not price but dependency: every piece of B2B logic goes through a third-party app, with its own subscription, limits and updates that can break the ordering flow.
The cost of a custom B2B store
Custom requires a heavier upfront investment, but recurring costs are lower and the business logic belongs to you.
| Custom item | 2026 range | Over 3 years |
|---|---|---|
| Initial build (catalogue, accounts, pricing, quotes) | EUR 45,000 to 110,000 | EUR 45,000 to 110,000 |
| Maintenance and changes (15% per year) | EUR 6,750 to 16,500 per year | EUR 20,000 to 50,000 |
| Cloud hosting and CDN | EUR 150 to 400 per month | EUR 5,400 to 14,400 |
| Native ERP connector | Included or EUR 8,000 to 15,000 | EUR 0 to 15,000 |
| Payment fees (Stripe, ACH) | 0.8 to 1.5% on cards | Variable |
| Estimated total | EUR 70,000 to 190,000 |
At mid-range, a EUR 75,000 project costs about EUR 115,000 over 3 years, i.e. EUR 30,000 to 70,000 less than an equivalent app-heavy Shopify Plus setup.
How to decide based on your sales logic
| Criterion | Shopify Plus | Custom |
|---|---|---|
| Mixed B2C and B2B sales | Very well suited | Possible, more expensive |
| Prices per pharmacy and buying group | Via app, limited | Native, unlimited |
| Negotiated quotes and sales approval | Third-party app | Built-in workflow |
| Time to launch | 8 to 12 weeks | 14 to 22 weeks |
| Ownership of code and data | Shopify platform | Full |
| Recurring cost | High and rising with apps | Stable |
The rule of thumb: if more than 30% of your orders go through a quote or a negotiated discount, custom is usually more profitable from year two.
Mini case study
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Helen, CEO of a dermatological cosmetics manufacturer in New York, sells to 850 pharmacies with 4 discount levels and quotes for buying groups. Her Shopify Plus estimate: EUR 2,140 subscription, EUR 750 of apps and EUR 500 of connector per month, plus EUR 35,000 setup. Over 3 years: 3,390 x 36 + 35,000 = EUR 157,040 (about $169,000), excluding theme maintenance.
Custom is quoted at EUR 80,000, plus EUR 12,000 maintenance and EUR 3,600 hosting per year. Over 3 years: 80,000 + 46,800 = EUR 126,800 (about $136,000). Savings: EUR 30,240, with a built-in quote workflow and code she owns.
FAQ
Does Shopify Plus handle B2B natively?
Yes, since 2023 Shopify Plus includes B2B features (company catalogues, payment terms). They cover about 70% of simple needs, but multi-step quotes and overlapping discounts still require apps at EUR 100 to 400 per month each.
Is custom riskier?
Risk is managed with precise specifications and delivery in 3 to 4-week increments. Require code ownership and a Git repository in your name from day one.
Can we migrate from Shopify Plus to custom later?
Yes, migrating products, customers and orders takes 3 to 6 weeks. Budget EUR 8,000 to 15,000 for data migration and SEO redirects.
What maintenance budget should we plan for custom?
Plan 12 to 18% of the initial cost per year. For an EUR 80,000 project, that is EUR 10,000 to 14,000 per year.
Which option launches fastest?
Shopify Plus goes live in 8 to 12 weeks, custom in 14 to 22 weeks. A two-phase launch lets you sell from week 10 with a reduced scope.
Let's scope your project. Share your pricing rules, order volume and ERP: we compare both options over 3 years with a costed budget and a schedule. 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.
