E-Commerce to ERP Integration: Keeping Your Online Store and Back-Office in Sync

You’re selling online. Orders come through Shopify or WooCommerce, payments land in Stripe or PayPal, and then someone on your team manually enters those orders into your accounting or ERP system. They update stock levels by hand. They create invoices. They reconcile the numbers at the end of the week and wonder why they never quite match.

If this sounds familiar, you’re not alone. The gap between a business’s online store and its back-office systems is one of the most common — and most costly — integration problems Australian businesses face. And the bigger your order volume grows, the wider that gap gets.

What Needs to Sync (and Why)

E-commerce to ERP integration isn’t a single connection. It’s several distinct data flows, each with its own timing, direction, and set of pitfalls.

Orders

This is the core flow. A customer places an order on your online store, and that order needs to appear in your back-office system — whether that’s Xero, MYOB, NetSuite, or a dedicated ERP. The order record should include line items, quantities, unit prices, shipping costs, discounts, and the correct GST treatment for each line.

Direction: Online store to ERP, one-way. Timing: As close to real-time as possible. Delayed order sync means delayed fulfilment.

Inventory

Stock levels need to stay consistent between your online store and your warehouse or ERP. When you sell a unit online, the ERP should reflect the reduction. When you receive new stock in the ERP, your online store should show the updated availability.

Direction: Two-way. ERP is the source of truth for stock levels, but the online store triggers reductions. Timing: Near real-time for stock reductions (to prevent overselling). Stock increases can tolerate a slight delay.

Customers

Customer records — name, email, shipping address, billing address — should flow from the online store to the ERP. For returning customers, the integration should match existing records rather than creating duplicates.

Direction: Online store to ERP, with optional updates flowing back (like customer credit limits or payment terms). Timing: Can be near real-time or batched. Less urgency than orders or inventory.

Payments and Refunds

Payment confirmations from your payment gateway (Stripe, PayPal, Afterpay) need to reconcile against invoices in your accounting system. Refunds need to flow through as credit notes. Partial refunds need to be handled without corrupting the original invoice.

Direction: Payment gateway to accounting system. Timing: Daily batch is usually sufficient. Real-time is better but not always necessary.

Common Integration Approaches

Native Connectors and Marketplace Apps

Shopify’s app store and WooCommerce’s plugin ecosystem both offer connectors to popular accounting and ERP platforms. Apps like A2X (for accounting reconciliation), Stock&Buy (for inventory), and various Xero/MYOB connectors handle standard workflows.

Pros: Fast setup, purpose-built for common scenarios, ongoing updates from the developer. Cons: Limited customisation, may not handle complex product structures (bundles, variants, kits), often charge per-order fees that scale with volume.

Middleware (Zapier, Make, Workato)

Middleware tools can bridge the gap between your store and ERP, especially for platforms that don’t have native connectors. You build automations that trigger on order events and push data to your back-office system.

Pros: Flexible, supports more platform combinations, no code required. Cons: Multi-line orders are awkward to handle, error recovery is limited, costs scale with volume, complex product/tax mapping requires workarounds.

Custom API Integration

A purpose-built integration that connects your store’s API directly to your ERP’s API, handling your specific product structures, pricing rules, tax logic, and workflow requirements.

Pros: Handles any complexity, proper error handling, no per-transaction fees, you own it. Cons: Higher upfront investment, requires development expertise.

The Tricky Parts Nobody Warns You About

Product Mapping

Your online store has SKUs. Your ERP has item codes. They might not match. Your store sells a “Bundle Pack” that doesn’t exist as a single item in your ERP — it’s three separate products that need to be picked individually. Your store has product variants (size, colour) that your ERP tracks differently.

Getting product mapping right is where most integrations either succeed or fall apart. Before you build anything, export your full product list from both systems and map them manually. Every SKU in the store needs a corresponding item (or items) in the ERP. Mismatches here mean wrong stock levels, wrong costs, and wrong financial reports.

GST and Tax Complexity

Australian GST seems straightforward until you integrate. Your online store might show GST-inclusive prices. Your ERP might work with GST-exclusive amounts. Some products are GST-free (certain food items, medical supplies, exports). If your integration doesn’t handle the conversion correctly, your invoices will be wrong and your BAS will be off.

Shipping and Discounts

Shipping charges and discount codes create accounting entries that need to land in the right accounts. A $10 discount on a $100 order isn’t the same as selling the product for $90 — the discount might need to appear in a separate account for reporting purposes. Shipping revenue (if you charge for it) is often a different revenue account from product sales. Free shipping promotions need to be handled as a zero-value line item, not omitted entirely.

Returns and Partial Refunds

A customer returns one item from a three-item order. Your online store processes the partial refund. Your ERP needs to: restore the stock for the returned item, create a credit note against the original invoice for the correct amount, and adjust the payment record. Most native connectors handle full refunds but struggle with partial refunds, exchanges, or store credit.

Multi-Channel Selling

If you sell through Shopify plus eBay plus Amazon plus a physical store, inventory sync becomes exponentially more complex. Each channel needs accurate stock levels, but a sale on one channel needs to reduce availability across all others — instantly. A centralised inventory system (your ERP) becomes the single source of truth, and each sales channel syncs against it.

Planning Your Integration

Before you start connecting systems, answer these questions:

1. What’s your order volume? Under 20 orders per day, a marketplace app might be sufficient. Over that, and the per-order fees and limitations start to hurt.
2. How complex is your product catalogue? Simple products with a 1:1 SKU mapping are easy. Bundles, kits, variants, and configurable products need careful planning.
3. How many sales channels? Single-channel is straightforward. Multi-channel requires a centralised inventory approach.
4. What’s your tolerance for delay? Can you accept a 15-minute sync interval, or does your fulfilment process need orders within seconds?
5. What happens when things go wrong? What’s your process for handling a failed sync, a duplicate order, or a stock discrepancy? Build this into the plan from day one.

The businesses that get e-commerce integration right are the ones that treat it as an operational project, not a technical one. The technology is the easy part. The hard part is mapping your actual business processes — with all their quirks, exceptions, and edge cases — into a reliable automated flow. Get that mapping right and the integration becomes the backbone of your operations. Get it wrong and you’ll spend more time managing the integration than you saved by building it.