The verdict in three sentences
For a Berlin SMB, Shopify is unbeatable at launch but its cost climbs with volume: subscription + commissions + apps eventually weigh heavily. Custom Medusa/Next.js is expensive to buy (35,000 to 70,000 EUR excl. VAT) but amortises and removes commissions. The tipping point sits around 500,000 EUR of annual GMV: below it, stay on SaaS; above it, custom becomes rational.
The three options costed in 2026
Each model has a different cost structure: recurring subscription + commission for Shopify, hosting + dev for WooCommerce, one-off + AMS for custom.
| Option | Initial cost (EUR excl. VAT) | Annual recurring (EUR excl. VAT) | Commission |
|---|---|---|---|
| Shopify Advanced | 0 - 3,000 (setup) | ~2,300 (sub) + apps 1,200 - 6,000 | 0.5 - 2 % outside Shopify Payments |
| WooCommerce | 8,000 - 20,000 | hosting 480 - 2,400 + maintenance 2,000 - 5,000 | 0 % |
| Custom Medusa/Next.js | 35,000 - 70,000 | AMS 6,000 - 18,000 | 0 % |
Shopify charges a commission on revenue if you don't use Shopify Payments. That line, invisible at first, becomes the dominant cost at high volume — which is where custom regains the edge.
The 3-year TCO by GMV
Let's compare total cost at two revenue levels, commissions included.
| Annual GMV | Shopify (3 yrs) | Custom (3 yrs) | Winner |
|---|---|---|---|
| 200,000 EUR | ~18,000 | ~63,000 | Shopify |
| 500,000 EUR | ~33,000 | ~70,000 | Shopify (edge) |
| 1,000,000 EUR | ~78,000 | ~76,000 | Custom |
| 2,000,000 EUR | ~150,000 | ~88,000 | Custom |
The Shopify figures include subscription, apps and a weighted average commission; custom includes build and AMS. Above ~1M EUR of GMV, the gap widens fast in favour of custom, not counting the functional freedom gained.
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Mini case study
Thomas runs an outdoor-gear SMB in Berlin, 900,000 EUR GMV in 2026, outside Shopify Payments with an effective commission of 1.3 %. He pays ~11,700 EUR/year in commission + 2,300 EUR subscription + 3,000 EUR apps = 17,000 EUR/year, i.e. 51,000 EUR over 3 years. A custom Medusa build at 55,000 EUR + AMS 9,000/year = 73,000 EUR over 3 years: still a bit more, but from year 4 it's only 9,000 EUR/year versus 17,000. The crossover happens at 3.5 years, and Thomas regains full control of his catalogue and checkout.
FAQ
At what revenue does custom become worthwhile? Around 500,000 EUR of GMV the maths balances; above 1M EUR, custom clearly wins over 3 years, especially outside Shopify Payments.
Is WooCommerce a good compromise? Yes for a standard catalogue and tight budget: 8,000 to 20,000 EUR of dev, no commission, but technical maintenance (updates, security) not to be underestimated.
Can we migrate from Shopify to custom later? Yes, and it's common. Plan a catalogue/customer/order data migration of 6,000 to 15,000 EUR depending on volume.
Is custom riskier? The risk is project-related (timeline, scope), not technical if the stack is proven (Medusa, Next.js). MVP-then-iterate staging keeps it under control.
Are Shopify commissions negotiable? They disappear with Shopify Payments, but that isn't always optimal on fees. Run the real numbers on your payment mix.
Let's scope your project. Send us your GMV, payment mix and functional needs: we simulate the 3-year Shopify vs custom TCO and recommend the right tier. 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.
