Shopify vs custom online store — what a subscription really costs
The Shopify vs custom online store decision comes down to three numbers: revenue, SKU count and how many integrations you need into warehouse, courier and accounting. Below €150K annual revenue Shopify is the cheaper option. Above €300K the transaction fees, checkout limits and the €27,600/year Shopify Plus subscription outpace the one-off cost of a custom online store. This page lays out the exact thresholds, hidden fees and the scenarios where a custom build pays back in 14-22 months versus Shopify Advanced or Plus.
When Shopify works and when it stops
Shopify fits a standard retail scenario: 50-500 products, one warehouse, two or three couriers, card payment. It breaks the moment you need B2B pricing tiers, multi-warehouse logic, more than 20,000 SKUs or a custom checkout flow for regulated goods. The same wall hits accounting — Shopify does not expose raw data without an app, and every app is another €15-€80/month.
- ✓Transaction fees on every order — 0.5% to 2% on revenue if you skip Shopify Payments, plus 1.5-2.9% card processing. On €300K revenue that is €4,500-€8,700/year that disappears with a custom online store.
- ✓App stack from €200 to €900/month — Klaviyo, ReCharge, Bold, Stocky, Shipstation, B2B portal. A typical Shopify Advanced store with 8-12 apps lands at €4,000-€10,000/year in SaaS alone.
- ✓Checkout you cannot edit on Basic and Advanced — without Shopify Plus there is no access to checkout.liquid, which means no custom pre-payment flow, VAT groups or fiscal document generation.
- ✓Vendor lock-in on theme and data — Liquid templates do not run outside Shopify, and the customer and order export is CSV without relational links. Migration to another platform takes 4-8 weeks of engineering.
- ✓API rate and webhook limits — 2 requests/second on Basic/Advanced, 4 on Plus. Syncing 15,000 SKUs from ERP takes 2+ hours for a full pass — impossible for a high-velocity catalog.
- ✓Shopify Plus starts at €2,300/month — €27,600/year before app fees and payments. For that money you get a custom software build with full checkout and data control, paid back in 12-18 months.
- ✓B2B features are premium-only — customer-specific catalog, price tiers, net terms and quote-to-invoice live in Shopify Plus B2B; without it you run 4-5 manual processes in spreadsheets.
Who each option fits
A starting D2C brand with 20-300 SKUs, one warehouse, one courier, revenue up to €150K/year. You run with 1-2 people, no ERP, no B2B clients, standard products at fixed prices. Shopify Basic at €36/month plus 3-4 apps lasts you 18-24 months before friction.
Revenue €150K-€500K, 500-3,000 SKUs, two warehouses, one B2B channel, accounting and courier API integrations. Shopify Advanced plus apps lands at €700-€1,200/month and custom starts to beat it on a 24-month horizon, especially with unique logistics.
Revenue above €500K, 5,000+ SKUs, multi-warehouse, B2B with pricing tiers, regulated goods (food, cosmetics, pharma) or a custom checkout with fiscal documents. Shopify Plus becomes an expensive ceiling — a custom Next.js + PostgreSQL build pays back in 14-22 months.
How we compare Shopify vs custom
We never recommend a path before seeing four numbers: annual revenue, average order value, SKU count and monthly orders. The audit takes 3-5 working days and ends with a 36-month TCO model in Excel.
1. Audit your current Shopify (if you have one)
We pull active apps, monthly fees, Shopify Payments percentages and API limits you hit. We compare checkout conversion and abandoned cart against your vertical median. We routinely find €300-€600/month in redundant apps doing 5% of what Shopify Advanced already does natively.
2. 36-month TCO model
We stack the Shopify subscription, app stack, Shopify Payments cut and theme development against the custom alternative: €18K-€45K one-off build, €120-€350/month hosting, 8-16 dev hours/month. Breakeven typically lands between month 14 and 26 above €300K revenue.
3. Custom tech stack
Next.js 15 + TypeScript on the front, PostgreSQL for catalog and orders, Stripe for payments, BunnyCDN for static assets, a clean API gateway for API integrations with carriers, ERP and accounting. Headless from day one, so a mobile app or marketplace channel ships without re-architecting.
4. Migration from Shopify to custom
We export products, variants, customers and orders, then 301-redirect every legacy URL into the new structure. SEO authority is preserved — Google sees no trust drop. The cutover takes 8-14 weeks with the last 2 weeks running both stacks in parallel. See how to connect your online store to warehouse and couriers for the integration playbook.
Why Saitami
Prices are fixed in EUR — no transaction fees, no app stack, no vendor lock-in. For the WordPress version of this same trade-off, see WooCommerce vs custom e-commerce, or the broader e-commerce overview.
Frequently Asked Questions
At what revenue does Shopify stop paying off?
Around €250K-€350K annual revenue on Shopify Advanced with 8-12 apps. Above that threshold, transaction fees (€2,500-€7,000), SaaS subscriptions (€4,000-€10,000) and an inevitable Shopify Plus upgrade (€27,600) exceed the amortized cost of a custom build at €25K-€45K over 36 months.
How much does a custom online store cost vs Shopify Plus?
A Saitami custom build starts at €18,000 for a standard B2C scenario with up to 2,000 SKUs, one warehouse, one payment provider and two courier integrations. A full B2B+B2C store with ERP and multi-warehouse runs €35,000-€60,000. Shopify Plus alone is €27,600/year before apps and transaction fees — the custom path pays back in 14-22 months.
How long does migration from Shopify to custom take?
8-14 weeks for a 1,000-5,000 SKU store. First 2-3 weeks are discovery and architecture, 4-7 weeks build, 1-2 weeks data migration and parallel run, final week DNS cutover with 301 redirects from every Shopify URL. SEO loss with correct execution stays under 5% and recovers in 4-8 weeks.
Will we lose Shopify's CDN speed and security?
No. A Next.js custom store runs on BunnyCDN or Cloudflare with edge caching in 60-100 locations — TTFB under 80ms for European traffic, on par with Shopify. PCI-DSS is covered by Stripe as payment intermediary; no card data touches your server. Application-level security is equal or higher because you no longer have 12 third-party apps reading your orders.
Can a custom store run B2B and B2C at the same time?
Yes, and this is one of the main reasons businesses leave Shopify. A custom build runs two paths on one core — /shop for retail with VAT-inclusive prices, /wholesale for B2B with net pricing, credit limits, quote-to-invoice flow and per-customer catalog. On Shopify the same setup requires Plus B2B (€2,300/month) or a parallel second store with double subscriptions.
Ready for a precise TCO model Shopify vs custom?
Send a link to your current Shopify store or a short description of revenue, SKU count and integrations. Within 5 working days you get a 36-month cost table and a breakeven analysis tailored to your numbers.
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