Integration Migration to Shopify

Last updated August 2026

Migrating third-party integrations including ERPs, CRMs, payment gateways, shipping providers, accounting systems, and marketing tools when moving to Shopify.

What transfers

• Integration logic can be recreated with Shopify apps
• Data flow patterns can be replicated

• Custom integration code does not transfer
• Platform-specific connectors are not compatible
• Historical sync data and logs
• Integration-specific configuration
• Webhook endpoints and authentication

Risks and common problems

• Critical business processes (inventory sync, order export) breaking
• Data synchronization gaps during transition
• Double-data entry in ERP during parallel run
• Real-time inventory discrepancies
• Accounting system reconciliation failures

Recommended approach

Audit all current integrations. Categorize into: 1) Replace with Shopify native (payment gateways, basic shipping). 2) Replace with Shopify app (ERP connectors, accounting, loyalty). 3) Rebuild with Shopify API (custom integrations). Plan a parallel-run period for critical integrations. Test data flow end-to-end before cutting over.

Technical notes

• Shopify App Store has connectors for most major ERPs
• Custom integrations use Shopify Admin API (REST or GraphQL)
• Webhook subscriptions replace platform-specific hooks
• Consider middleware/iPaaS (Zapier, Make, Tray.io) for integration gaps
• API rate limits differ between platforms
• Plan for data format differences between old and new integrations

Platform-specific guides

Integration Migration by platform:

References

• Shopify App Store — Shopify