Moving your B2B eCommerce operation from Magento to Shopify Plus isn’t just a platform switch—it’s a business transformation. The right Magento to Shopify data migration strategy protects your customer relationships, preserves complex pricing structures, and eliminates constant maintenance headaches.

This B2B Shopify migration direction walks through transferring products, customer hierarchies, and transaction data from Magento to Shopify Plus. Whether you’re running a 5,000 SKU catalog with multi-tier pricing or managing hundreds of wholesale accounts, we’ll show you how to migrate B2B data Magento to Shopify while keeping your business running smoothly.

Why B2B Brands Are Moving from Magento to Shopify Plus

The shift from Magento to Shopify Plus accelerates every quarter. Enterprise B2B brands are tired of expensive developer dependencies, security patches, and infrastructure management. Here’s why the Magento to Shopify Plus migration makes sense for B2B operations.

Maintenance Costs and Developer Dependency

Magento requires constant technical oversight. Security patches arrive monthly. Extensions break after updates. Most Magento stores need a dedicated development team just to keep running.

Annual costs add up:

  • Developer salaries or agency retainers: $60,000–$150,000+
  • Hosting and infrastructure: $2,000–$10,000+ monthly
  • Extension licenses: $5,000–$20,000 annually
  • Security audits: $10,000–$30,000 annually

Shopify Plus eliminates this overhead. The platform handles security, updates, and infrastructure with a predictable monthly fee.

Shopify’s Integrated B2B Suite

Shopify Plus includes native B2B functionality—no plugins required. The platform supports company profiles, custom pricing, net payment terms, and self-serve customer portals. These Shopify Plus B2B features rival what Magento offers through extensions.

Native capabilities include:

  • Company records with multiple user accounts
  • Custom price lists and Shopify B2B pricing tiers per customer
  • Purchase order checkout and net payment terms
  • Quote requests and approval workflows
  • Tax exemption management
  • Multi-location inventory allocation

Everything works together because it’s built into the platform, not stitched together from third-party plugins.

Security, Speed, and Scalability

Shopify Plus handles millions of transactions daily. The platform scales automatically during traffic spikes, giving B2B customers fast page loads whether ordering 10 items or 10,000.

Security is built in: PCI DSS Level 1 compliance, automatic SSL, fraud detection, and 99.99% uptime. You’re not managing server security or SSL certificates.

Pro Tip: Shopify Plus supports multi-location inventory, customer-specific pricing, and ERP integrations natively. Features requiring expensive custom development on Magento are standard on Shopify Plus.

For more on why B2B businesses choose Shopify Plus, see Why Shopify Plus Is the Best Ecommerce Platform for B2B.

How to Migrate B2B Data from Magento to Shopify Plus

What Is the Recommended Way to Transfer All Products, Customers, and Orders from Magento to Shopify?

The recommended approach combines automated tools for bulk data with manual configuration for B2B-specific features. You can’t simply export Magento data and import it unchanged—Shopify uses different data structures, especially for B2B functionality.

Here’s the proven process:

Phase 1: Export and clean your Magento data

  • Export products, including all variants, images, and custom attributes
  • Export customer records with account types and group assignments
  • Export order history with payment and shipping details
  • Document custom pricing rules, tiered discounts, and tax configurations

Phase 2: Transform data for Shopify’s structure

  • Map Magento product attributes to Shopify metafields
  • Convert customer groups to Shopify company profiles
  • Restructure pricing tiers for Shopify’s price list system
  • Prepare CSV files following Shopify’s import format

Phase 3: Import to Shopify Plus

  • Import products using Matrixify or Shopify’s bulk import
  • Create company profiles and assign customers
  • Configure custom pricing and catalogs
  • Set up payment terms and tax exemptions

Phase 4: Validate and test

  • Verify all products imported with correct pricing
  • Test customer login and B2B portal access
  • Place test orders for each customer segment
  • Confirm integrations with ERP and accounting systems

Exporting Products, Customers, and Orders

Start with a complete data export from Magento:

Products and SKUs: Product names, descriptions, pricing (base, tiered, customer group-specific), images, inventory quantities, product relationships, and custom attributes.

Customers and accounts: Customer names, emails, company names, customer group assignments, address book entries, tax exemption status, credit limits, and payment terms.

Orders and transactions: Order numbers, dates, line items, payment methods, shipping details, order status, fulfillment history, and customer notes.

Export from Magento’s database or built-in export tools. Clean the data—remove test accounts, outdated products, and duplicates.

Mapping Customer Groups to Shopify B2B Companies

Magento’s customer groups don’t directly translate to Shopify’s company structure. In this Magento to Shopify data migration step, you’ll map groups to company profiles.

In Magento, you might have groups like “Wholesale,” “Distributor,” “Retail,” and “VIP.” On Shopify Plus, these become company records with assigned Shopify B2B pricing tiers.

Create a mapping document:

  • Magento group “Wholesale Level 1” → Shopify company with Price List A (15% discount)
  • Magento group “Distributor” → Shopify company with Price List B (25% discount)
  • Magento group “Retail Partner” → Shopify company with Price List C (10% discount)

Each Shopify company can have multiple users. If your Magento groups include individual buyers, create company records and invite users to join them.

Transferring Custom Pricing, Tiered Discounts, and Catalogs

Magento’s pricing rules are flexible but complicated. Shopify Plus uses price lists—simpler but powerful.

Converting tiered pricing:

Magento: “Buy 10-49 units at $50, 50-99 at $45, 100+ at $40”

Shopify approach:

  1. Create separate price lists for volume tiers
  2. Assign customers to appropriate lists based on typical order size
  3. Use Shopify Flow to automate price list changes

Alternatively, use apps like Bold Custom Pricing for dynamic tier pricing.

Converting customer group catalogs:

If certain customers only see specific products in Magento, replicate this with Shopify’s catalog assignment. Create catalogs for different segments and assign them to companies.

Migrating Tax Rules, Quotes, and Invoices

Tax rules: Export your Magento tax configurations. Set up corresponding rules in Shopify Plus using native tax settings or apps like Avalara AvaTax for complex scenarios. Configure tax exemptions for wholesale customers at the company level.

Quotes: Magento’s quote-to-order workflow doesn’t have a direct Shopify equivalent. Use draft orders for quote functionality, or integrate apps like Quotify or SparkLayer for full quote management.

Invoices: Historical invoices stay in Magento for record-keeping. Going forward, Shopify Plus generates invoices automatically. Integrate with accounting software like QuickBooks or NetSuite to maintain continuity.

Data type Migration method Tool / Integration
Products & SKUs CSV / Matrixify Matrixify, LitExtension
Customers & orders API / bulk import Cart2Cart, Shopify API
Pricing tiers App / manual setup B2B by Shopify
Quotes / invoices Integration QuickBooks, NetSuite

For a detailed walkthrough of the Magento migration process, see How to Migrate Your Magento Ecommerce Shop to Shopify.

B2B Features Native to Shopify Plus

Shopify Plus includes comprehensive B2B Shopify migration tools and features.

Company Profiles & Multi-User Accounts

Create company records representing your B2B customers. Each company can have multiple user accounts with different permission levels, shared cart, company-specific payment terms, assigned catalogs and price lists, and purchase order approval workflows.

Users can be assigned roles: admin, buyer, or location-specific buyer. Admins manage users and view all orders. Buyers place orders but can’t manage the account.

Price Lists and Custom Catalogs

Create unlimited price lists with custom pricing for products or variants. Assign price lists to companies so each customer sees their negotiated rates automatically.

Example: Standard retail price is $100. Create Price List A: $85 (15% off) for wholesalers, Price List B: $75 (25% off) for distributors, Price List C: $90 (10% off) for retail partners.

Custom catalogs let you show different products to different customers.

Net Payment Terms and PO Checkout

Enable net payment terms (Net 30, Net 60, etc.) for B2B companies. Customers place orders without immediate payment. Support purchase order numbers during checkout—Shopify Plus captures this and includes it on order documents.

Self-Serve Portals for B2B Clients

B2B customers get their own portal showing order history, company users and permissions, payment terms, and reorder functionality. This reduces support inquiries.

Pro Tip: Shopify Plus allows up to 10,000 company records natively with full API control.

To stay current with the latest B2B capabilities, read What’s New in Business-to-Business with Shopify. For a real-world example of successful B2B migration, see our State Forty Eight case study.

Custom Pricing and Account Structures

How Can I Migrate My Entire Magento Store Database to Shopify, Including Customers and Transaction History?

Migrating your entire Magento database requires careful planning and the right tools. Here’s the complete process:

Step 1: Prepare your Magento data

Run a full database backup. Export all data tables you need to migrate:

  • Product catalog with all attributes
  • Customer accounts with addresses
  • Order history with line items
  • Custom fields and metadata

Clean the data—remove test records, spam accounts, and outdated information. The cleaner your data going in, the smoother the migration.

Step 2: Choose your migration tool

For complete database migrations, you’ll need professional migration services or tools like:

  • LitExtension: Handles full store migrations, including order history
  • Cart2Cart: Automated migration with SEO preservation
  • Matrixify: Powerful for product data but requires more manual setup
  • Custom API scripts: For very large or complex databases

Step 3: Map Magento structures to Shopify

Document how Magento elements translate to Shopify:

  • Customer groups → Company profiles
  • Custom options → Metafields
  • Configurable products → Variants
  • Category trees → Collections
  • CMS pages → Shopify pages

Step 4: Execute the migration

Run the migration in a development store first. Never migrate directly to your live store. Test thoroughly:

  • Verify product data accuracy
  • Check customer account access
  • Review order history completeness
  • Test B2B pricing and payment terms

Step 5: Validate and go live

Compare record counts between Magento and Shopify. Every product, customer, and order should have migrated. Address any discrepancies before switching your DNS.

How to Replicate Magento’s Tiered Pricing Model

Magento’s tier pricing is rule-based. Shopify Plus uses price lists assigned to companies or customer tags.

Option 1: Price lists per tier

Create multiple price lists for different tiers: Standard (retail), Tier 1 (small wholesale), Tier 2 (large wholesale), Tier 3 (distributor). Use Shopify Flow to automatically upgrade customers when they hit volume thresholds.

Option 2: Dynamic pricing apps

Apps like Bold Custom Pricing provide quantity-based discounts similar to Magento.

Option 3: Hybrid approach

Use price lists for major segments and Shopify Scripts for additional quantity-based adjustments at checkout.

Setting Up Dynamic Discounts or Customer Tags

Customer tags in Shopify work like Magento’s customer attributes. Tag customers based on:

  • Purchase volume (“VIP,” “High-Value”)
  • Customer type (“Wholesale,” “Retail”)
  • Region (“West Coast,” “International”)
  • Account status (“Net 30,” “Prepay”)

Use these tags to:

  • Show/hide products or collections
  • Apply automatic discounts via Shopify Scripts
  • Segment email marketing campaigns
  • Create filtered customer lists

Shopify Flow can automatically apply or remove tags based on customer behavior, order history, or other triggers.

Mapping Magento Customer Groups to Shopify Companies

We covered this briefly earlier, but here’s the detailed mapping process:

Step 1: List all Magento customer groups

Export a report showing:

  • Group name
  • Number of customers
  • Associated pricing rules
  • Product visibility rules

Step 2: Design Shopify company structure

Decide which Magento groups become Shopify companies with price lists vs. which become customer tags.

Generally:

  • True B2B accounts (businesses placing orders) → Shopify companies
  • Loyalty tiers (individuals with special pricing) → Customer tags with discounts

Step 3: Create company records

For each B2B account, create a company in Shopify. Import company details via CSV or API:

  • Company name
  • Tax exemption status
  • Payment terms
  • Assigned price list
  • Assigned catalog

Step 4: Invite and assign users

Send invitations to customer email addresses. They’ll set up accounts and be automatically linked to their company. Multiple employees from one business can access the same company account.

Managing Tax-Exempt and Wholesale Customers

Shopify Plus handles tax exemptions at the company level. Mark companies as tax-exempt during setup. Their orders automatically exclude taxes at checkout.

For wholesale customers who need specific tax treatment:

  • Set tax exemptions at the company level
  • Use tax overrides for specific products or regions
  • Integrate tax automation software like Avalara or TaxJar for complex scenarios

Configure tax exemption certificates if required in your jurisdiction. Store documentation in company notes or use apps that manage exemption certificates.

Key Integrations for Shopify Plus B2B

B2B operations need integration between eCommerce, ERP, CRM, and other systems. These shopify b2b api integrations make Shopify Plus work with your existing infrastructure.

ERP: NetSuite, Microsoft Dynamics, Brightpearl

ERP integration synchronizes inventory levels, order data, customer credit limits, invoices, and accounting transactions.

Popular integrations: NetSuite: Farapp, Celigo, Commercient | Microsoft Dynamics: Cloudfy, eSync | Brightpearl: Native integration | SAP Business One: APPSeCONNECT

Choose an integration partner experienced with ecommerce platform migration and B2B requirements.

CRM: HubSpot, Salesforce, Zoho

Connect your CRM to track customer interactions, sync contact records, track order history for account managers, and trigger automated follow-ups.

Integration options: HubSpot: Native Shopify app | Salesforce: MuleSoft, Commercient, custom API | Zoho CRM: Native integration

PIM: Plytix, Akeneo

Product Information Management centralizes product data for catalogs with thousands of SKUs and multiple channels.

Benefits: Single source of truth, automated Shopify updates, multi-language content management, enriched product information.

Popular PIM integrations: Plytix: Pre-built connector | Akeneo: Custom API | Salsify: Native support

Analytics: GA4, Looker Studio

Track B2B customer behavior, conversion funnels, and revenue attribution with Google Analytics 4, Looker Studio dashboards, and product analytics tools. Configure tracking to separate B2B and B2C transactions.

For guidance on setting up analytics during migration, see What You Need to Know About Google Analytics 4 Migration and Shopify.

For detailed integration guidance, check Shopify B2B services.

Tools and Services for Data Migration

Which Magento to Shopify Data Migration Plugins Ensure No Data Loss and Maintain Site Performance?

Professional migration tools reduce data loss risk. Here are the top options for Magento to Shopify data migration.

Matrixify (Best for Large Catalogs): Handles massive catalogs with complex variants and metafields. Supports bulk product imports, customer data, order history, multi-location inventory, and custom metafields. Best for stores with 10,000+ SKUs. Requires technical knowledge.

LitExtension (Safe, Automated Migration): Provides automated Magento to Shopify Plus migration with minimal manual work. Handles products, customers, order history, SEO data, and images. Best for mid-sized stores. Pricing: $300-$2,000+.

Cart2Cart (Full Data + SEO Mapping): Specializes in preserving SEO. Migrates all data, URL redirects, customer passwords, and product reviews. Best for SEO-focused migrations. Volume-based pricing.

Shopify Transporter (Legacy Support): Shopify’s official tool for Plus merchants. Open-source, free, requires technical expertise. Handles products, customers, and custom transformations. Best for developers.

Pro Tip: Always test data integrity in a development store before switching DNS. Run parallel operations for 1-2 weeks.

Common Pitfalls During B2B Migration

Even with the best tools, ecommerce platform migration in B2B projects faces challenges.

Loss of Custom Pricing Logic

Magento’s pricing rules are flexible. Shopify’s native pricing is more straightforward. You’ll need to simplify pricing logic, use apps for complex scenarios, document rules that can’t migrate directly, and manually recreate VIP pricing agreements. Audit Magento pricing rules before migration.

Incomplete Order History Transfer

Order history is crucial for B2B relationships. Common issues: API timeouts on large databases, custom order fields that don’t map, lost line item notes, and missing shipping costs or taxes. Validate a sample of orders post-migration.

Misaligned Tax or Currency Data

Tax calculations differ between platforms. Reconfigure custom tax rules or tax automation services on Shopify. For multi-currency sales, set up Shopify Payments or use apps like Bold Multi-Currency. Test checkout in all currencies.

API Timeouts on Large Databases

Shopify’s API has rate limits. Solutions: Use batch imports with rate limiting, migrate data in segments, work with experienced agencies, and use Shopify Plus’s higher API limits.

For project scoping guidance, see Migrating to Shopify: Project Scoping & Discovery Expectations.

Cost and Timeline for B2B Data Migration

What Is the Cost and Process for Turnkey Magento to Shopify Data Migration for Large Inventories?

The cost of Magento to Shopify enterprise migration depends on catalog size, customization complexity, and service level.

Migration Type Cost Range Timeframe
Automated tool migration $800–$2,000 1–2 weeks
Hybrid (manual + tool) $2,000–$5,000 3–4 weeks
Full-service agency migration $5,000–$15,000+ 4–8 weeks

Automated tool migration: Works for straightforward stores with standard products and simple pricing.

Hybrid migration: Combines automated data transfer with manual B2B configuration.

Full-service agency migration: Provides end-to-end support including data migration, theme development, B2B setup, integrations, testing, and launch support.

The Process for Turnkey Migration

Week 1-2: Discovery – Audit Magento setup, document features, design Shopify architecture, choose integrations, create migration plan.

Week 3-4: Setup – Set up Shopify Plus, configure B2B features, install apps, set up integrations, create or customize theme.

Week 5-6: Data Migration – Export Magento data, transform for Shopify, import products/customers/orders, configure pricing and catalogs.

Week 7: Testing – Test B2B workflows, place test orders for each segment, verify integrations, check SEO and redirects, train team.

Week 8: Launch – Final data sync, switch DNS, monitor for issues, provide support.

For launch day details, see Migrating to Shopify: Launch Day Expectations.

Can I Hire an Expert to Handle a Secure and Complete Magento to Shopify Data Migration Service?

Yes. Professional migration services ensure data security, minimize downtime, and reduce the risk of data loss. Here’s what to look for when hiring:

Experience with B2B migrations: Not all Shopify developers understand B2B requirements. Choose partners with proven experience in ecommerce platform migration B2B projects.

Magento expertise: Your agency should understand Magento’s data structures, not just Shopify. They need to extract data properly and map it to Shopify correctly.

Security practices: Ask about data handling procedures. Are exports encrypted? How is sensitive customer data protected during transfer?

References and case studies: Request examples of similar migrations. How large were the catalogs? Did they handle multi-tier pricing? What was the timeline?

Post-launch support: Migration doesn’t end at launch. You’ll need support for weeks afterward as issues surface and customers adjust to the new platform.

Fyresite specializes in Magento to Shopify Plus B2B migrations. We’ve successfully migrated enterprise catalogs while maintaining complex pricing structures, customer hierarchies, and ERP integrations. Our team handles everything from data extraction through post-launch optimization.

Check out our migration case studies from Magento to Shopify Plus:

For comprehensive B2B guidance, see The Ultimate Playbook for B2B on Shopify and B2B Shopify and You: Using Shopify as a B2B Platform.

For expert guidance throughout your migration, see our 10 Top Tips for a Smooth Shopify Migration and The Beginner’s Guide to Shopify Migration. Also, check Shopify Myths to separate fact from fiction about the platform’s capabilities.

Request a quote for your Magento to Shopify Plus B2B migration today: Contact our team for a customized migration plan and timeline.

Final Checklist: Magento to Shopify B2B Data Migration

Here’s your complete checklist for a successful Magento to Shopify data migration:

Before Migration:

  • [ ] Audit Magento store (products, customers, orders, custom features)
  • [ ] Export all data and create backups
  • [ ] Document custom pricing rules and customer groups
  • [ ] Choose Magento to Shopify data migration tools and services
  • [ ] Set up Shopify Plus development store
  • [ ] Configure B2B features and company structure
  • [ ] Install required apps, including shopify b2b api integrations

During Migration:

  • [ ] Import products with variants and metafields
  • [ ] Create company profiles and assign customers to migrate B2B data Magento to Shopify
  • [ ] Set up price lists and custom catalogs
  • [ ] Migrate order history
  • [ ] Configure payment terms and tax exemptions
  • [ ] Set up ERP and CRM integrations
  • [ ] Create 301 redirects for SEO

After Migration:

  • [ ] Validate product data accuracy
  • [ ] Test customer login and B2B portal access
  • [ ] Place test orders for each pricing tier
  • [ ] Verify integration data flows
  • [ ] Train team on Shopify Plus B2B features
  • [ ] Monitor site performance and fix issues
  • [ ] Provide customer communication and support

Ongoing:

  • [ ] Monitor order processing and fulfillment
  • [ ] Track customer feedback and issues
  • [ ] Refine pricing and catalog assignments
  • [ ] Improve site performance based on analytics
  • [ ] Plan future enhancements and optimizations

A successful Magento to Shopify enterprise migration transforms your B2B operations. You’ll reduce maintenance costs, improve customer experience, and scale more easily. With the right migration strategy and tools, you can move your entire database while maintaining business continuity.

The key to a flawless Magento to Shopify data migration is proper planning, choosing the right tools, and working with experts who understand both platforms. Whether you handle migration yourself with automated tools or partner with a full-service agency, follow this checklist to ensure nothing falls through the cracks.

Ready to move your B2B store to Shopify Plus? Contact Fyresite for expert migration services that protect your data and preserve your customer relationships. Need ongoing support after migration? Check out our Shopify Maintenance and Support services.

For more on optimizing your Shopify Plus store post-migration, explore:

Get your Shopify Plus B2B migration checklist and start planning your move today. Download our free toolkit with migration planning templates, data validation checklists, and integration guides to ensure your Magento to Shopify data migration succeeds from start to finish.