E-commerce11 min read

Custom vs SaaS B2B E-Commerce: 3-Year Cost Comparison (2026)

Mohamed Bah·Fondateur, Kolonell
October 10, 2026
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Custom vs SaaS B2B E-Commerce: 3-Year Cost Comparison (2026)

Custom vs SaaS B2B E-Commerce: 3-Year Cost Comparison (2026)

E-commerce

The verdict in three sentences

Over 3 years, SaaS B2B (Shopify B2B, Sana Commerce) and custom builds land in similar ranges, between 105,000 and 240,000 EUR excl. VAT. SaaS wins when your commercial rules are standard and you want to go live in 3 months. Custom wins as soon as pricing, configurators or ERP integration fall outside the box, and becomes clearly cheaper from the fourth or fifth year.

Three quotes, three cost logics

The CIO of an industrial distributor typically receives three proposals that cannot be compared line by line. SaaS mostly charges recurring licences, custom mostly charges an upfront investment. Here are 2026 orders of magnitude for a distributor with 8,000 SKUs, 2,500 customer accounts and an ERP such as Sage X3, Microsoft Dynamics or SAP Business One.

ItemShopify B2B (Plus)Sana CommerceCustom
Annual licence or subscription25,000 to 32,000 EUR40,000 to 60,000 EUR0 EUR
Annual apps and connectors6,000 to 12,000 EURLargely included0 EUR
Integration and setup30,000 to 45,000 EUR30,000 to 50,000 EUR80,000 to 160,000 EUR
Annual maintenance and evolutions8,000 to 15,000 EUR6,000 to 12,000 EUR15% of build, 12,000 to 24,000 EUR
Annual hostingIncludedIncluded4,000 to 9,000 EUR
Time to launch3 to 4 months4 to 5 months5 to 7 months
Code ownershipNoNoYes

Shopify Plus also charges variable fees on volume above a revenue threshold. For 6 M EUR of online sales, budget 0.25 to 0.40% depending on the contract, to be checked line by line with the vendor.

Total cost over 3 years, then 5 years

Scenario (EUR excl. VAT)Year 13-year total5-year total
Shopify B2B, low end69,000147,000225,000
Shopify B2B, high end104,000222,000340,000
Sana Commerce, mid range100,000218,000336,000
Custom at 80,000 EUR84,000116,000148,000
Custom at 120,000 EUR125,000171,000217,000
Custom at 160,000 EUR169,000235,000301,000

Assumptions: custom maintenance at 15% of build from year 2, hosting at 4,000 to 9,000 EUR a year, flat SaaS licences (in practice, expect 3 to 7% yearly increases). Over 3 years, the gap stays small. Over 5 years, a mid-range custom build costs more than 100,000 EUR less than an equivalent Sana Commerce setup.

The criteria that really decide

Pricing complexity. Net prices per customer, discounts per product family, annual contracts, delivered prices per zone: Sana handles ERP-driven prices well, Shopify B2B covers company-specific catalogues but quickly hits limits on combined rules. Beyond five stacked rules, custom becomes simpler.

ERP integration. Sana Commerce is built around Dynamics and SAP, which sharply reduces integration risk. With a less common ERP or an in-house system, the SaaS advantage disappears.

Vendor lock-in. With SaaS, the roadmap, price increases and reversibility are out of your hands. Require a full data export (customers, orders, content) in the contract and 6 months' notice on pricing changes.

Timeline. If a trade show or a contract end forces a launch within 4 months, SaaS is often the only realistic option.

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You are :

Thomas, CIO of an industrial supplies distributor in Nantes (6 M EUR online sales target, Sage X3 ERP), compares a Sana quote at 45,000 EUR annual licence plus 40,000 EUR integration, and a custom quote at 120,000 EUR plus 18,000 EUR yearly maintenance and 6,000 EUR hosting.

Over 3 years, Sana costs 45,000 × 3 + 40,000 + 9,000 × 3 maintenance = 202,000 EUR. Custom costs 120,000 + 18,000 × 2 + 6,000 × 3 = 174,000 EUR. The 28,000 EUR gap widens to about 90,000 EUR over 5 years. Thomas still weighs timing: custom needs 6 months versus 4. He picks custom with a first release limited to catalogue, net prices and quick reorder, delivered in 4 months for 85,000 EUR.

FAQ

Does Shopify B2B suit an industrial distributor?

Yes for a catalogue under 10,000 SKUs with simple per-customer catalogues. Budget 25,000 to 32,000 EUR a year for the Plus licence and 6,000 to 12,000 EUR of annual apps.

Why is custom maintenance set at 15%?

It is the 2026 order of magnitude to cover fixes, security updates and small evolutions, so 12,000 to 24,000 EUR a year for an 80,000 to 160,000 EUR build. Below 10%, the platform ages fast.

Can we migrate from SaaS to custom later?

Yes, provided data export was negotiated. A migration usually costs 20,000 to 40,000 EUR excl. VAT on top of the new build.

What timeline for a custom build?

5 to 7 months for a full scope, 3 to 4 months for a first release covering catalogue, net prices and quick ordering.

How do we compare two quotes fairly?

Bring everything back to a total cost over 3 and 5 years, with the same assumptions for licence increases (5% a year) and volume. Add the exit cost to each scenario.

Let's scope your project. Share your three quotes and your ERP: we will build a comparable 3- and 5-year total cost and price a custom alternative between 80,000 and 160,000 EUR excl. VAT, delivered in 5 to 7 months. Detailed quote within 48 h. WhatsApp +221 77 596 93 33.

Tags:#B2B e-commerce#custom vs SaaS#total cost of ownership#Shopify B2B#industrial distributor#2026 comparison
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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.