Shopify ERP Integration

Shopify is the platform most often connected to custom ERPs, and it has a well-documented integration surface. This page summarizes how that surface works and what it means for ERP synchronization. Statements marked as documented come from Shopify’s developer documentation (see sources); statements marked as recommendation are our architectural guidance.

How Shopify connects to an ERP

An ERP integration is built as a Shopify app — a custom app for a single store, or a distributed app for many. The app authenticates with an access token and uses two mechanisms:

• The GraphQL Admin API to read and write orders, products, inventory, customers, fulfillments, and refunds. Documented: Shopify labels the REST Admin API as legacy and has required new public apps to use GraphQL exclusively since April 1, 2025.
• Webhooks to be notified of changes. Documented: webhooks can be delivered over HTTPS, to Amazon EventBridge, or to Google Cloud Pub/Sub.

Recommendation: place a small integration service between Shopify and the ERP rather than calling Shopify directly from the ERP. It isolates retry logic, rate-limit handling, and mapping from both systems. See the architecture guide.

Common integration use cases

• Exporting web orders to the ERP for fulfillment, invoicing, and accounting.
• Publishing stock levels from the ERP or warehouse system to the store.
• Publishing products, variants, and prices from the ERP or a PIM.
• Sending shipment confirmations and tracking numbers back to Shopify.
• Recording refunds as credit notes in the ERP.
• Synchronizing B2B customers, price lists, and payment terms (often on Shopify Plus).

Order synchronization

Documented: order-related webhook topics include orders/create, orders/paid, orders/updated, and orders/cancelled, plus refunds/create. The orders query supports filtering by updated_at, which enables checkpoint-based reconciliation.

Recommendation: choose the export trigger based on when your ERP should see the order (on creation or on payment), fetch the full order through the API before mapping, and store the Shopify order ID as a unique external reference in the ERP. Detailed steps are in How to Synchronize Shopify Orders with an ERP.

Inventory synchronization

Documented: Shopify tracks inventory per inventory item (one per variant) per location, in states including available, on_hand, committed, reserved, incoming, damaged, safety_stock, and quality_control. on_hand is the sum of available, committed, reserved, damaged, safety stock, and quality control. The committed state is managed by Shopify and cannot be adjusted through the API. The inventorySetQuantities mutation supports compare-and-swap, and from API version 2026-04 requires an idempotency key through the @idempotent directive.

Recommendation: treat the ERP as the owner of physical stock, publish a calculated sellable quantity, and account for orders Shopify has accepted that have not yet reached the ERP. See inventory synchronization.

Product and variant synchronization

Documented: products have variants; each variant has an associated inventory item, which carries the SKU and inventory tracking settings.

Recommendation: map each Shopify variant to one ERP article through a unique, stable SKU, and store Shopify’s product, variant, and inventory item IDs in a cross-reference table. If the ERP is the product master, create and update products from it and keep merchandising fields (descriptions, images, SEO) owned by Shopify. See mapping products to ERP SKUs.

Customer data synchronization

Documented: orders reference a customer, and customers can be read and written through the Admin API. Shopify Plus includes B2B features such as companies and company locations.

Recommendation: for B2C stores, many ERPs work best with a single generic web customer and addresses stored on each order, which avoids duplicate customer records. For B2B, match customers on a stable ID stored in both systems, never on email alone. Treat customer data as personal data: sync only the fields the ERP needs.

Fulfillment and shipment updates

Documented: Shopify models fulfillment work through fulfillment orders — groups of items to be fulfilled from the same location. Fulfillments are created against fulfillment order line items with fulfillmentCreate, which accepts tracking company, numbers, and URLs, and a notifyCustomer flag.

Recommendation: create fulfillments when the warehouse confirms shipment, use the ERP shipment ID to make the call idempotent, and choose one system to send shipping notifications. See shipment tracking sync.

API and webhook considerations

Documented:

• Webhooks must be answered within five seconds; failed deliveries are retried up to eight times over four hours, after which the subscription is removed if failures persist.
• Webhook ordering is not guaranteed, duplicates should be ignored using X-Shopify-Webhook-Id, and Shopify recommends reconciliation jobs instead of relying solely on webhooks.
• Webhooks are signed with an HMAC in the X-Shopify-Hmac-Sha256 header.
• The GraphQL Admin API is rate-limited by calculated query cost in a leaky-bucket model; the bucket size and restore rate vary by API and plan. A single query has a maximum cost.
• The GraphQL Admin API can return HTTP 200 for requests that failed, including throttled requests, so errors must be read from the response body.
• API versions are released quarterly; each stable version is supported for at least 12 months.

Recommendation: see handling Shopify webhooks reliably and webhooks vs. polling for Shopify.

Common implementation challenges

• Overselling because sync overwrites Shopify stock without accounting for in-flight orders.
• Duplicate ERP orders from duplicate webhooks or retries after timeouts.
• Tax and discount differences when the ERP recalculates rather than copies Shopify’s values.
• Removed webhook subscriptions after an outage, discovered only when orders stop arriving.
• Rate-limit pressure during catalog-wide updates; use bulk operations and request minimal fields.
• API version upgrades missed until a version is retired.

Direct integration vs. middleware

Shopify integrations are commonly built three ways: a custom integration service, an iPaaS or middleware platform, or a prebuilt connector for a specific ERP. For a custom ERP, prebuilt connectors rarely exist, so the choice is usually between a custom service and middleware with custom adapters. The direct vs. middleware comparison explains the trade-offs, and the architecture planner suggests a starting point for your situation.