Custom Software for E-commerce: When Shopify Isnt Enough

Shopify is brilliant for the first 5 years of most e-commerce businesses. Past a certain scale or complexity, the platform that helped you get started starts limiting you. App-by-app workarounds compound. Theme customisation hits a wall. Checkout flow is constrained by what Shopify allows. Custom B2B pricing, complex inventory, and integrated operations get expensive.

Here are five signs your e-commerce business has outgrown Shopify, and what custom alternatives cost.

1. You're paying $2k+/month in Shopify Plus + apps

Shopify Plus starts at $2,500/month. Add the apps you actually need (Klaviyo, Recharge, Yotpo, Returnly, custom reporting, AI personalisation, etc.) and the monthly bill compounds. At $7–12k/month all-in, custom infrastructure pays back in year 2–3.

2. Your checkout doesn't fit Shopify's UI

Shopify constrains checkout deeply. If you need custom shipping logic, multi-step checkout, complex payment options, B2B credit terms, or wholesale signup flows — you're either limited by Shopify or paying for extensive customisation that doesn't survive platform updates.

3. Your B2B pricing is too complex

Per-customer pricing, contract-based pricing, volume tiers, regional pricing, promotional stacking — Shopify B2B handles some of this, but workflows often require workarounds. Custom commerce platforms handle complex pricing natively.

4. Your inventory isn't fitting

Bundles, kits, configurable products with attributes, made-to-order, drop-ship hybrid, multi-warehouse with smart routing — generic e-commerce inventory often forces workarounds. Custom platforms model your actual inventory.

5. Your operations are integrated elsewhere

If your ERP, warehouse, or accounting is custom or heavily-customised, integrating Shopify becomes a constant maintenance tax. Custom e-commerce that natively integrates with your other custom systems eliminates this friction.

What it costs

Lean replacement of Shopify ($80–160k): Single-store, standard checkout, basic B2B. 12–16 week build.

Multi-store / mid-market ($180–350k): Multiple stores, sophisticated checkout, complex B2B pricing, custom inventory, full ERP integration. 18–28 week build.

Enterprise commerce platform ($400–800k+): Multi-region, multi-language, B2C + B2B unified, custom OMS, multiple fulfillment paths, headless architecture. 28–40 week build.

The middle path

Many companies don't replace Shopify entirely — they build custom for specific needs (B2B portal, customer dashboard, custom checkout, custom ERP integration) while keeping Shopify for catalogue/cart. This hybrid often makes more sense than full replacement.

The break-even logic: if your monthly Shopify + apps spend exceeds $5–7k and you have specific differentiating workflows Shopify can't accommodate, the custom case is strong.

For a transparent cost estimate for your specific e-commerce scope, our cost calculator runs 5 questions. Or see our post on the real cost of SaaS customisation for the longer thinking.