When mid-market to enterprise companies evaluate Shopify vs Magento for B2B, they’re defining their digital commerce trajectory for the next 5-10 years. This comparison examines Shopify vs Magento for B2B through what actually matters: ERP integration, total cost of ownership, B2B functionality, and scalability. Drawing on Atwix’s implementation experience with both platforms, we’ll show you exactly when each platform wins.
Shopify vs Magento for B2B: Quick Comparison
| Factor | Shopify Plus | Adobe Commerce (Magento) |
|---|---|---|
| Best For | Speed to market, hybrid B2B/B2C | Complex customization, enterprise scale |
| Implementation | 3-6 months | 6-12 months |
| 3-Year TCO (Mid-Market) | $139,000 | $236,000 |
| B2B Features | Native + apps | 16 native features |
| ERP Integration | Middleware solutions | Deep native connectivity |
| Customization | Framework-limited | Unlimited open-source |
| Hosting | Fully managed | Self-managed or cloud |
The Core Philosophy: Managed vs. Open-Source
Shopify Plus delivers enterprise B2B through a fully managed, hosted infrastructure. You get automatic updates, built-in security, and auto-scaling. Implementation takes 3-6 months with Liquid developers handling customizations within Shopify’s framework.
Adobe Commerce (Magento) provides complete control over every aspect of your B2B operation. Its open-source foundation allows unlimited customization and deep enterprise integration. Implementation requires 6-12 months with senior PHP developers.
B2B Functionality: Built-In vs. Customizable
| B2B Feature | Shopify Plus | Adobe Commerce (Magento) |
|---|---|---|
| Company Hierarchies | Basic | Unlimited Levels |
| Custom Catalogs | Via apps | Native real-time pricing |
| Quote Management | Third-party | Multi-round built-in |
| Purchase Approvals | Limited | AI-powered routing |
| Credit Management | Basic terms | Comprehensive tracking |
Shopify Plus B2B Capabilities
Shopify Plus offers solid B2B functionality through native features and apps:
- B2B checkout with wholesale pricing
- Company accounts with basic hierarchies
- Payment terms and installments
- Customer-specific pricing via Shopify Scripts
- Bulk ordering through apps
Magento B2B Features
Magento’s 16 native B2B capabilities include:
- Advanced company hierarchies with unlimited levels
- Custom catalogs with customer-specific visibility
- Quote management with multi-round negotiations
- Purchase order approvals with AI-powered routing
- Company credit management
- Requisition lists supporting up to 999 lists per user
For Reinders, a B2B turf distributor, Atwix implemented Adobe Commerce with ElasticSuite search, delivering lightning-fast product discovery and seamless checkout for large orders.
ERP Integration: The Hidden Complexity
B2B operations require real-time data flow, including inventory levels, custom pricing, order status, and credit limits.
| ERP System | Shopify Plus | Adobe Commerce (Magento) |
|---|---|---|
| SAP | Middleware (4-8 weeks) | Native modules (8-16 weeks) |
| NetSuite | Native apps (3-4 weeks) | Integration (6-10 weeks) |
| Microsoft Dynamics | Third-party (4-8 weeks) | Pre-built (8-12 weeks) |
Shopify wins for: Mid-market companies with straightforward ERP connections and 1,000-5,000 monthly orders.
Magento wins for: Enterprises with multiple ERP instances and complex workflow requirements.
Total Cost of Ownership: 3-Year Reality
Mid-Market Manufacturer (1,000-5,000 orders/month)
Shopify Plus: $72K platform + $27K transaction fees + $40K development = $139,000
Adobe Commerce: $66K licensing + $36K hosting + $80K implementation + $54K maintenance = $236,000
Enterprise Distributor (10,000+ orders/month)
Shopify Plus: $72K platform + $90K transaction fees + $120K customization = $282,000
Adobe Commerce: $150K licensing + $60K hosting + $200K implementation + $90K maintenance = $500,000
At enterprise scale, Adobe Commerce’s pricing becomes competitive relative to functionality, while Shopify Plus transaction fees can exceed $90K annually on $50M+ GMV.
Migration Considerations: Switching Between Platforms
Shopify to Magento Migration
Companies typically migrate from Shopify to Magento when customization requirements exceed Shopify’s framework, integration complexity demands open-source flexibility, or transaction volumes make Shopify fees prohibitive.
Timeline: 6-9 months for mid-sized catalogs
Key considerations: Custom app functionality must be rebuilt; ERP connections reconfigured
Magento to Shopify Migration
Companies occasionally migrate from Magento to Shopify when the technical overhead becomes unsustainable, or their business models shift toward a hybrid B2B/B2C model that requires faster deployment.
Timeline: 4-6 months with functionality assessment
Key considerations: Complex custom features may not translate; ongoing dependency on apps
When Shopify Plus Wins
- Rapid deployment (under 6 months)
- Hybrid B2B/B2C operations
- Minimal technical team required
- Predictable costs
- Modern, mobile-first checkout
Perfect for: Mid-market B2B brands prioritizing speed-to-market and businesses wanting minimal technical overhead.
When Magento Wins
- Complex customization beyond frameworks
- Deep ERP integration with real-time sync
- Multi-brand, multi-storefront operations
- Unlimited scalability for high volumes
- Advanced B2B workflows (quotes, approvals, credit)
Perfect for: Enterprise distributors, manufacturers with complex pricing structures, and multinational operations.
Real-World Results: Shopify Plus vs Adobe Commerce
PowerPak: Shopify Plus Success
When PowerPak, a leading safety equipment distributor, needed rapid B2B deployment, Atwix implemented Shopify Plus with custom wholesale capabilities.
Results:
- 230% revenue growth** in 12 months
- 3-month implementation** (versus 12-month Magento estimate)
- 6% operational cost reduction** through Shopify’s managed infrastructure
- Zero downtime** during seasonal peak (100K+ orders/quarter)
Why Shopify Plus Won: PowerPak prioritized speed-to-market and minimal technical overhead. Shopify’s managed infrastructure eliminated hosting complexity, while native B2B features + apps covered 90% of requirements.
Reinders: Magento Enterprise Performance
When Reinders, a B2B turf distributor with 50K+ SKUs, needed custom product configurators and complex pricing logic, Atwix built on Adobe Commerce.
Results:
- Sub-2-second page loads** on 50K SKU catalog (ElasticSuite search)
- Custom product configurator** (impossible within Shopify framework)
- Real-time ERP sync** with NetSuite (inventory + custom pricing)
- Unlimited scalability** for 10K+ monthly orders
Why Magento Won: Reinders required customization beyond Shopify’s framework; specifically, SKU-level custom pricing pulled from NetSuite ERP, and a visual product configurator for complex turf/irrigation products.
The Atwix Advantage: True Multi-Platform Expertise
Most agencies specialize in one platform. Atwix brings certified expertise in both, which fundamentally changes how we approach Shopify vs Magento for B2B decisions.
Our credentials:
- Adobe Commerce Contributor Partner with 300+ certifications
- Shopify Partner with proven enterprise implementations
- #1 Magento contributor globally
- Real implementations on both platforms at scale
This dual expertise means we recommend the platform that genuinely fits your business, and not the one we happen to specialize in.
Making Your Platform Decision
| Your Priority | Recommended Platform |
|---|---|
| Speed to market | Shopify Plus |
| Total customization control | Magento |
| Hybrid B2B/B2C | Shopify Plus |
| Complex ERP integration | Magento |
| Predictable costs | Shopify Plus |
| Multi-brand operations | Magento |
Partner With Platform Experts Who Know Both
Choosing between Shopify vs Magento for B2B shapes your digital commerce future. The wrong decision can lead to costly re-platforming and a competitive disadvantage.
Atwix helps mid-market and enterprise B2B companies make platform decisions backed by real implementation experience on both Shopify Plus and Adobe Commerce. We build systems designed to scale with your business for years to come, whether that means Shopify’s managed simplicity or Magento’s unlimited flexibility.
Ready to discuss your platform decision? Contact Atwix’s B2B eCommerce specialists to explore which platform future-proofs your business.