Introduction
"Should we use Shopify or build something custom?"
This question comes up in nearly every conversation with e-commerce entrepreneurs. The answer isn't as straightforward as platform comparison articles suggest. It depends on your products, your customers, your growth plans, and your tolerance for trade-offs.
Both options can work brilliantly. Both can also become expensive mistakes. The difference lies in understanding what each approach actually offers—beyond the marketing promises—and honestly assessing your needs.
This guide breaks down the real considerations for choosing between Shopify and custom e-commerce development. We've built successful stores on both platforms—from Shopify-powered skincare brands to fully custom solutions—so we understand the trade-offs firsthand.
Understanding Your Options
Shopify: The Managed Platform
Shopify is a fully hosted e-commerce platform that handles the technical infrastructure while you focus on selling. You get:
- A ready-to-use storefront
- Built-in payment processing
- Hosting and security managed for you
- An app ecosystem for extending functionality
- Themes for customizing appearance
Shopify serves over 4 million stores, from small businesses to enterprise brands like Gymshark and Allbirds.
Custom E-commerce: Built for You
Custom e-commerce means building your store from the ground up, typically using frameworks like:
- Headless commerce (Shopify Storefront API, CommerceJS, Medusa)
- Full-stack frameworks (Nuxt/Next.js with custom backend)
- Traditional platforms (WooCommerce, Magento) heavily customized
Custom doesn't mean starting from zero—it means assembling components to match your specific requirements.
When Shopify Makes Sense
You're Launching Quickly
If time-to-market is critical, Shopify wins. A competent team can launch a professional store in weeks, not months. The platform handles countless decisions for you—checkout flow, payment security, inventory management—so you can focus on products and marketing.
Your Products Are Straightforward
Standard physical products with simple variations (size, color) work perfectly on Shopify. The platform's built-in product management handles these cases elegantly without customization.
You Don't Have Technical Resources
Shopify's app ecosystem means you can add functionality without developers. Need email marketing? Install Klaviyo. Need subscriptions? Install Recharge. Need reviews? Install Judge.me.
For non-technical founders, this self-service model is genuinely empowering.
Your Budget Is Constrained
A basic Shopify store with a premium theme costs under $5,000 to launch. Monthly fees start at $39. For businesses without capital for custom development, Shopify provides a professional solution at an accessible price point.
You Want Proven Conversion Optimization
Shopify's checkout has been optimized across millions of transactions. Small improvements in checkout conversion translate to millions in additional revenue at Shopify's scale—so they invest heavily in testing and refinement.
Beating Shopify's checkout with a custom implementation requires significant expertise and ongoing optimization.
When Custom E-commerce Makes Sense
You Have Unique Business Logic
Some businesses can't fit into Shopify's models:
- Complex pricing rules: B2B pricing that varies by customer, quantity breaks, negotiated contracts
- Custom product configurations: Build-your-own products with interdependent options
- Unique fulfillment requirements: Multi-vendor marketplaces, dropshipping with complex routing
- Industry-specific workflows: Prescription requirements, regulatory compliance, specialized approvals
If your business logic requires extensive workarounds on Shopify, custom development may actually be simpler.
Brand Experience Is Your Differentiator
Shopify themes offer customization, but within constraints. If your brand requires truly unique interactions—custom animations, innovative product visualization, immersive storytelling—a custom build provides unlimited creative freedom.
Premium brands often choose custom development specifically because they don't want their store to feel like a template.
You Need Deep Integrations
While Shopify apps cover common needs, complex integrations with enterprise systems (ERP, custom inventory management, legacy databases) often require custom development anyway. If you're building significant custom code on top of Shopify, the platform's benefits diminish.
Scale Economics Favor Custom
Shopify's pricing scales with revenue. On the basic plan, transaction fees (if not using Shopify Payments) add 2% to every sale. Advanced plans reduce fees but increase monthly costs.
At high volume, these fees can exceed the cost of maintaining custom infrastructure. A $10 million/year business on Shopify's Basic plan pays $200,000+ in transaction fees alone.
You Want Full Control
Custom development means you control:
- Your technology stack and hosting
- Your data (not mediated through a platform)
- Your feature roadmap (not dependent on Shopify's priorities)
- Your checkout experience (no "Powered by Shopify" constraints)
For some businesses, this control is worth the additional complexity.
The True Cost Comparison
Shopify Costs (Realistic)
Platform fees:
- Basic: $39/month
- Shopify: $105/month
- Advanced: $399/month
- Plus: $2,000+/month
Transaction fees:
- 2.9% + 30¢ with Shopify Payments
- Additional 0.5-2% without Shopify Payments
Apps:
- Premium theme: $250-400 (one-time)
- Essential apps: $100-500/month (email, reviews, upsells, etc.)
- Advanced apps: $500-2000/month (subscriptions, B2B, etc.)
Professional services:
- Theme customization: $2,000-15,000
- Custom app development: $5,000-50,000+
- Ongoing support: $500-2,000/month
Realistic Year 1 cost for a serious store: $15,000-50,000+
Custom E-commerce Costs (Realistic)
Initial development:
- Simple custom store: $30,000-75,000
- Complex custom store: $75,000-250,000+
- Enterprise solutions: $250,000+
Infrastructure:
- Hosting: $100-1,000/month
- CDN/caching: $50-500/month
- Security/monitoring: $100-500/month
Payment processing:
- Stripe/similar: 2.9% + 30¢ (no additional platform fees)
Ongoing development:
- Bug fixes/maintenance: $1,000-5,000/month
- Feature development: Project-based
Realistic Year 1 cost: $50,000-150,000+
The Break-Even Point
Custom development's higher upfront cost pays off when:
- Transaction fees exceed custom development costs
- Platform limitations require extensive workarounds
- You need capabilities Shopify can't provide
For most businesses doing under $1 million/year, Shopify's total cost of ownership is lower. Above $5 million/year, custom development often becomes economically attractive—assuming you have the technical resources to execute well.
The Hybrid Approach: Headless Commerce
You don't have to choose entirely. Headless commerce separates the frontend (what customers see) from the backend (commerce engine).
Shopify as a Headless Backend
Use Shopify's Storefront API to power a completely custom frontend:
- You get Shopify's reliable cart, checkout, and order management
- You get unlimited frontend flexibility
- You avoid building e-commerce infrastructure from scratch
Brands like Allbirds and FIGS use this approach—Shopify's backend reliability with custom frontend experiences.
When Headless Makes Sense
Headless is worth considering when:
- You need custom frontend experiences but want proven commerce infrastructure
- You're already on Shopify but hitting customization limits
- You have development resources to build and maintain a custom frontend
The trade-off: increased complexity. You're responsible for frontend performance, security, and maintenance that Shopify's hosted themes handle automatically.
Making the Decision
Choose Shopify If:
- You're launching a new store and need to move fast
- Your products and pricing are relatively standard
- You don't have dedicated technical resources
- Your annual revenue is under $2-3 million
- You prefer proven solutions over custom experimentation
Choose Custom If:
- Your business model has genuinely unique requirements
- Brand experience is a key differentiator
- You have technical resources (in-house or reliable partners)
- Platform fees significantly impact your margins
- You need integrations that don't exist as Shopify apps
Choose Headless If:
- You need custom frontend experiences
- You want Shopify's commerce infrastructure
- You have resources to maintain a decoupled architecture
- You're migrating from Shopify but want to preserve backend investment
Questions to Ask Yourself
- What makes my business unique? If your answer is about marketing, brand, or products—Shopify works. If it's about how you sell, custom may be necessary.
- What's my realistic budget? Include ongoing costs, not just launch costs. Be honest about what you can sustain.
- Do I have technical resources? Custom development requires ongoing technical investment. If you can't maintain it, you'll create problems. Read our guide on how to choose the right web development agency if you're considering outsourcing.
- What's my growth trajectory? Platform economics change at different scales. Plan for where you'll be in 2-3 years.
- What are my non-negotiables? Some requirements are hard constraints. Identify them early.
Conclusion
The Shopify vs. custom debate often frames as "simple vs. powerful" or "cheap vs. expensive." Reality is more nuanced.
Shopify is a sophisticated platform that powers billion-dollar brands. Custom development can be cost-effective at the right scale with the right team. The best choice depends on your specific situation—your products, your customers, your resources, and your ambitions.
Don't choose based on what successful brands use. Choose based on honest assessment of your needs, capabilities, and constraints. The right platform is the one that helps you serve customers better while remaining sustainable for your business.
If you're genuinely uncertain, starting with Shopify and migrating later is a valid strategy. You'll learn what your business actually needs—not what you imagine it needs—and make a more informed decision when the time comes.
The platform matters less than execution. A well-run Shopify store outperforms a poorly-maintained custom build every time.
Still deciding between Shopify and custom? Get in touch for a free consultation. We'll help you evaluate your specific needs and recommend the right approach—whether that's a polished Shopify store, a custom-built solution, or something in between. Explore our web development services or see our e-commerce work for examples.