Why connect Shopify to an ERP?
Shopify handles the storefront — product pages, checkout, payments, shipping. But once an order is placed, the back-office work begins: creating invoices, updating inventory, recording payments, handling returns. Most Shopify merchants do this manually at first, exporting CSVs or copying data between systems. It works when you process a handful of orders per day. At higher volumes, it becomes a source of errors and wasted time.
Connecting Shopify to your ERP automates this entire chain. Orders flow from Shopify into the ERP automatically. Inventory updates in near real-time so the store reflects actual stock. Invoices are created without manual entry. Payouts from Shopify Payments, Klarna, or Stripe are matched against invoices and marked as paid.
The result: less manual work, fewer errors, and financial data that stays current without daily reconciliation.
What data flows between Shopify and an ERP?
The specific data depends on which ERP you use, but a typical Shopify–ERP integration covers these flows:
Orders → ERP. Every new Shopify order is created as a sales order or invoice in the ERP. Line items, discounts, tax amounts, shipping costs, and customer details are mapped to the correct accounts and fields.
Inventory ← ERP. The ERP is usually the stock master. Inventory levels flow from the ERP to Shopify, keeping product availability accurate. This prevents overselling — especially important if you sell through multiple channels.
Refunds → ERP. When a Shopify refund is processed, a credit invoice is created in the ERP and linked to the original transaction.
Payouts → ERP. Payment provider settlements are reconciled against invoices. Provider fees (Shopify Payments, Klarna, Adyen, Stripe) are recorded as costs.
Products ↔ Both. Article data — names, SKUs, prices, descriptions — can sync in either direction depending on where you manage master data. Many merchants manage products in the ERP and push updates to Shopify.
Customers ↔ Both. Customer records sync between systems to avoid duplicates and keep contact information consistent.
Which ERP systems integrate with Shopify?
Junipeer supports connecting Shopify with a range of ERP systems. The right choice depends on your location, company size, and industry:
Nordic ERP systems
- Fortnox — the most popular ERP among Swedish small and mid-sized businesses. Handles orders, invoices, credit invoices, and payouts. See the Shopify–Fortnox setup guide for step-by-step instructions. - Visma.net — cloud ERP for Nordic mid-market companies. Stronger in multi-entity and multi-currency scenarios. See the Visma integration guide. - Visma Business — available on request for businesses already running Visma Business. - 24SevenOffice — Norwegian cloud ERP used by SMBs across the Nordics. - Specter — Nordic ERP with strong warehouse capabilities.
International ERP systems
- Business Central — Microsoft's cloud ERP, widely used across Europe and North America. - Brightpearl — retail-focused ERP built specifically for ecommerce and wholesale. - SAP — enterprise ERP for larger organizations. - NetSuite — coming soon. - Pyramid — available on request.
Not sure which ERP fits? The general ecommerce ERP integration guide covers how to evaluate your options.
How the integration works
With Junipeer, you connect Shopify and your ERP without building a custom solution or installing multiple apps. The setup process:
1. Connect both systems. Log into Junipeer and authorize your Shopify store and your ERP. Shopify uses OAuth — you approve the connection in the Shopify admin. Most ERP systems use API keys.
2. Choose your flows. Select which data should sync: orders, inventory, customers, refunds, payouts. Each flow can be enabled independently.
3. Configure data mapping. This is where the real work happens. You define how Shopify data maps to your ERP: which tax rates correspond to which tax codes, which payment methods map to which accounts, how shipping costs are recorded. For ERP systems like Fortnox, this means mapping to specific account numbers and cost centers.
4. Test with real orders. Run test transactions through the integration before going live. Verify that orders appear correctly in the ERP, that tax amounts are right, and that inventory updates flow back.
5. Go live and monitor. Activate the integration for production traffic. Junipeer provides logs and alerts so you can spot issues early. Failed syncs are automatically retried.
The technical connection takes about 15 minutes. The mapping and configuration depends on how complex your ERP setup is — a straightforward Fortnox setup might take an hour, while a multi-entity Business Central environment takes longer.
Common considerations for Shopify merchants
Multi-channel inventory. If you sell on Shopify plus marketplaces (Amazon, Zalando) or other channels, inventory management gets critical. The ERP should be the single source of truth for stock levels, pushing updates to all channels.
Shopify POS. If you use Shopify POS for physical retail alongside your online store, both channels create orders that need to reach the ERP. An integration handles both sources.
Tax configuration. Shopify calculates tax at checkout based on the customer's location. Your ERP needs matching tax codes. For EU sellers using OSS (One Stop Shop), this means country-specific tax accounts in the ERP.
Payment reconciliation. Shopify Payments, Klarna, and other providers settle funds on their own schedule, with fees deducted. The integration can match these settlements against invoices automatically — but you need to configure which accounts receive fees and settlements.
Apps and customizations. Shopify's app ecosystem means merchants often have custom fields, metafields, or third-party apps that affect order data. Make sure your integration handles these correctly, especially for subscription apps or custom discount logic.
Historical data. Decide whether to migrate historical Shopify orders into the ERP or start fresh from the integration go-live date. Most merchants start fresh and keep historical data in Shopify.
Next steps
Ready to connect? Check if your Shopify + ERP combination is available among Junipeer's integrations. We support 25+ systems and new connectors are added regularly.
Already on Fortnox? Start with the Shopify–Fortnox setup guide for detailed instructions.
Want to understand the broader picture first? Read the ecommerce ERP integration guide.