Shopify integrations that keep orders, stock and the books in agreement.
Shopify takes the order. Your ERP, accounting system and warehouse have to agree about it afterwards. Our Shopify integration services connect them so orders, inventory, refunds and payouts move without re-keying, and a mismatch reaches a person the same day instead of turning up at month end.
On this page
What we connect Shopify to
- ERP and accounting: NetSuite, QuickBooks, Xero and Microsoft Dynamics 365.
- CRMs: HubSpot and Salesforce, so the customer record includes what they bought.
- Warehouses and 3PLs, for fulfillment, tracking numbers and stock counts.
- Other sales channels and point-of-sale systems that share the same inventory.
- Your data warehouse or pricing tools.
The flows that usually matter
- Orders into the ERP or accounting system, with tax, discounts, shipping and gift cards mapped to the right accounts.
- Inventory from the ERP or warehouse back to Shopify, per location, often enough that you don't oversell.
- Fulfillment and tracking numbers back to Shopify, so the customer gets the shipping email.
- Refunds and returns into the books as credit memos, linked to the original sale.
- Payouts reconciled: each Shopify Payments payout matched to the orders, refunds and fees inside it, and to the deposit that reaches your bank.
Payout reconciliation is the flow stores most often leave manual, and it can take up much of the month-end close.
Shopify's API has moved to GraphQL
Shopify made its REST Admin API a legacy API on October 1, 2024. From April 1, 2025, new public apps submitted to the Shopify App Store must use the GraphQL Admin API, and Shopify's new features are built for GraphQL first.
For you, that means two things. Anything new should be built on GraphQL, which also has bulk operations for exporting years of orders without hitting rate limits. And if an older custom integration still calls the REST API, it's worth knowing before Shopify sets a date for it, because Shopify has said migration timelines for existing apps will be announced separately.
App Store app or custom integration
| Option | Good for | Watch out for |
|---|---|---|
| An app from the Shopify App Store | Standard orders and inventory into a popular ERP | Per-order pricing at volume, fixed field mapping, and how it reports a failed sync |
| An integration platform such as Celigo or Boomi | Several systems, and a team that will own the platform | Subscription cost, and logic spread across flows |
| Custom code on the GraphQL Admin API | Bundles, subscriptions, B2B price lists, several stores, or rules the apps can't express | It has to be built and maintained, and it should be yours |
If an app does the job, we will tell you, and help you set it up. For NetSuite specifically, see our NetSuite integrations page. For QuickBooks, see QuickBooks integrations.
How we build a Shopify integration
- Webhooks deliver changes as they happen, and a scheduled reconciliation catches anything a webhook missed.
- Each order, refund and payout is keyed on its Shopify ID and applied once, however many times it arrives.
- Large backfills run as bulk operations, so they don't compete with your live store's API traffic.
- Orders that fail validation in the ERP wait in a review queue with the ERP's error attached.
- A daily report compares order counts, revenue and stock between Shopify and each connected system.
The same pattern is on our custom API integrations page.
Pricing decisions still made in spreadsheets
Some stores have the data flowing and still can't answer which product to push tomorrow. For a retailer with 500 products, whose pricing decisions took twelve hours a day in spreadsheets, we built the analytics layer that answers it. Read the case study.
What it costs
One store, one ERP and standard orders is a small project. Several stores or regions, B2B pricing, subscriptions, a 3PL and payout reconciliation is a larger one. We fix the price once the integration inventory exists. For market figures, see what custom software development costs.
The Automation Audit
One workflow you name, mapped end to end, with the arithmetic done before anyone writes code.
- Scope
- One workflow you choose, traced end to end, including the steps nobody documented.
- Duration
- Two weeks, fixed.
- Fee
- Fixed, and quoted in full before we start. No hourly drift.
- You get
- A written map: what can be automated, what it would save in hours, what building it would cost, and what we would leave alone.
- You keep it
- The map is yours whether or not you hire us to build anything.
And if the audit shows the automation will not pay for itself inside twelve months, we will tell you, and we will not quote the build.
Questions we get asked about Shopify integrations
Do we need Shopify Plus?
No. The Admin API is available on every plan. Plus adds things like more stores under one organization and some B2B features, which change the design but aren't required for an integration.
Can you connect several Shopify stores to one ERP?
Yes. Each store is a separate connection, and the integration maps each one to the right subsidiary, location or price list in the ERP.
Where does Shopify Flow fit?
Shopify Flow is good for automations inside the store, such as tagging orders or alerting staff. We use it for those and keep the ERP and accounting sync in code that can be tested and reconciled.
What happens during a sale, when order volume spikes?
Orders queue and are processed in order. The integration slows down to stay within Shopify's and the ERP's limits instead of failing, and the queue drains as the spike passes.
