Custom E-commerceVSShopify Plus

Custom E-commerce vs Shopify Plus

Compare custom e-commerce development vs Shopify Plus. Analyze features, transaction fees, and total cost of ownership for high-growth online retailers.

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Feature Comparison

Compare capabilities between custom e-commerce and Shopify Plus.

Feature	Custom E-commerce	Shopify Plus
Custom Checkout Flow Fully customizable checkout		Limited
Transaction Fee Freedom No platform transaction fees		0.2-0.4%
Headless Architecture Decoupled frontend/backend		Hydrogen only
Custom Product Logic Complex configurators & bundles		Apps
Multi-Currency Native True multi-currency support
B2B Capabilities Wholesale/B2B functionality		B2B add-on
Inventory Management Multi-location inventory
API Flexibility Custom API endpoints		GraphQL/REST
Performance Control Full performance optimization		Platform limits
Data Ownership Complete data portability		Exportable

Paying $2,300-$40,000/month in Shopify Plus fees?

Custom e-commerce eliminates platform fees entirely.

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Cost Analysis

Pricing & TCO Analysis

Compare realistic costs based on actual Shopify Plus pricing.

Custom E-commerce

Initial Setup$75,000 - $250,000

Monthly Platform Fee$0

Transaction Fees$0 (payment processor only)

Annual at $5M GMV$25,000 - $60,000

App/Plugin CostsBuilt-in

5-Year TCO ($5M GMV)$200,000 - $550,000

5-Year TCO$200,000 - $550,000

Shopify Plus

Initial Setup$25,000 - $100,000

Monthly Platform Fee$2,300 - $40,000/mo

Transaction Fees0.2-0.4% (+ processor)

Annual at $5M GMV$57,600 - $508,000

App/Plugin Costs$500 - $5,000/mo

5-Year TCO ($5M GMV)$413,000 - $2,690,000

5-Year TCO$413,000 - $2,690,000

Potential Savings with Custom E-commerce

$213,000 - $2,140,000

over 5 years compared to Shopify Plus

Advantages & Disadvantages

Understand the benefits and trade-offs.

Custom E-commerce

Advantages

Zero platform transaction fees
Complete checkout customization
True headless flexibility
Build any product configurator
No monthly platform fees
Full performance control

Disadvantages

Higher upfront development cost
3-6 month development timeline
Requires ongoing maintenance
No app marketplace

Shopify Plus

Advantages

Quick launch (weeks, not months)
Extensive app ecosystem
Built-in enterprise features
Proven scalability
Regular platform updates

Disadvantages

Transaction fees on every sale
Monthly fees increase with scale
Checkout customization limited
Platform constraints on architecture
App costs add up quickly

Which is Right for You?

Consider these scenarios for your decision.

Choose Custom E-commerce if you...

High GMV Business

$5M+ annual sales where fees add up

Custom Product Experience

Complex configurators or bundles

Headless Requirements

Need true frontend flexibility

Unique Checkout Needs

Subscription, B2B, or custom flows

Choose Shopify Plus if you...

Quick Launch Needed

Need to sell within weeks

Standard E-commerce

Typical B2C product sales

App Ecosystem Needed

Want access to Shopify apps

Limited Technical Team

Prefer managed platform

Migration Path

Migration Timeline

Plan your migration from Shopify Plus to custom.

2-3 weeks

Discovery & Planning

Analyze current store, data, and requirements

2-4 weeks

Architecture Design

Design custom platform architecture and integrations

10-16 weeks

Core Development

Build storefront, checkout, and admin

2-3 weeks

Data Migration

Products, customers, orders, and content migration

2-4 weeks

Integration Setup

Payment, shipping, ERP connections

2-3 weeks

Testing & Launch

QA, performance testing, go-live

Total Migration Timeline

20-33 weeks

Migration Benefits

Zero downtime migration strategy
Complete order history preservation
SEO equity maintained with redirects
Customer accounts migrated seamlessly
Post-launch optimization support

Stop Paying Transaction Fees on Every Sale

Custom e-commerce keeps more profit in your pocket. Let's analyze your current Shopify Plus costs.

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Our Solutions

Explore Our E-commerce Solutions

Custom platforms for online retail success.

E-commerce CRM

Customer management built for online retail.

Customer segmentation
Purchase history
Marketing automation

Learn more

E-commerce Analytics

Advanced analytics for conversion optimization.

Funnel analysis
Customer LTV
Attribution modeling

Learn more

Inventory & Fulfillment

Warehouse management for e-commerce operations.

Multi-location inventory
Order routing
Shipping optimization

Learn more

View All Solutions

Comparison

Shopify Plus starts at $2,300/month but scales with GMV—high-volume merchants pay $2,300 or 0.25% of GMV (whichever is higher), capped around $40,000/month. Plus 0.2-0.4% transaction fees. A $5M/year store pays $57,600-$508,000 annually. Custom e-commerce has zero ongoing platform fees.

Shopify Plus charges 0.2% on Shopify Payments, 0.4% if using third-party payment providers. On $5M GMV, that's $10,000-$20,000/year in platform transaction fees alone, on top of payment processor fees. Custom platforms only pay processor fees (typically 2.5-2.9% + $0.30).

Yes. Custom platforms can include all Shopify Plus features: multi-currency, multi-location inventory, B2B wholesale, automation workflows, and more. The difference is you build exactly what you need without paying for unused features or being constrained by platform limitations.

Shopify's app ecosystem is convenient but costly—popular apps run $100-$500/month each. Custom development builds these features natively, eliminating ongoing app fees. Reviews, subscriptions, bundles, and other common app functions are built into your platform.

Shopify Plus limits checkout customization to Checkout Extensibility apps and scripts. Complex flows (multi-step, conditional logic, embedded subscriptions) hit walls. Custom platforms have zero checkout constraints—build exactly the conversion flow your business needs.

Custom development takes 3-6 months vs Shopify Plus's 4-8 weeks. However, you're not retrofitting workarounds later. Many brands launch on Shopify, hit constraints at scale, then migrate to custom—costing more than building custom initially.

Knowledge Base