Integrating Shopify With Your Business Systems: Beyond the App Store

Shopify makes it easy to start selling online. But the moment your business grows beyond a handful of daily orders, Shopify becomes one part of a larger system — and that system needs to work together.

Your accounting software needs to know about every sale. Your inventory system needs stock levels updated instantly. Your CRM needs customer data for follow-up. Your fulfilment team needs orders routed and tracked. And if you’re selling through multiple channels, all of them need consistent data.

Shopify’s App Store has thousands of plugins promising to handle this. Some are genuinely good. But most businesses eventually discover that plugins solve 80% of the problem and leave the remaining 20% — the hard, business-specific 20% — unresolved.

What Needs to Connect

Accounting (Xero, MYOB, QuickBooks)

Every Shopify order needs to appear in your accounting system. Each order has line items, discounts, shipping charges, taxes, and potentially refunds — all needing correct account codes.

Popular connectors like A2X handle this well for standard setups. For most businesses under 500 orders per month with straightforward products, an off-the-shelf tool is genuinely sufficient.

Where it breaks down: custom pricing rules, complex discount structures, mixed GST products (some taxable, some GST-free in the same order), and multi-currency transactions.

Inventory Management

This is where things get genuinely difficult. Shopify has built-in inventory tracking, but it’s basic — single-location stock counts, no batch tracking, no serial numbers, no bill of materials.

If you’re managing inventory through a dedicated system like Cin7, DEAR, or Unleashed, you need two-way sync. Shopify sells a unit, the inventory system reduces stock. The warehouse receives new stock, Shopify updates availability.

The real-time challenge: a 15-minute delay means you could sell products already out of stock. During high-traffic periods, even 5 minutes creates overselling risk.

CRM and Marketing

Shopify captures customer data but it’s not a CRM. If you’re using HubSpot, Klaviyo, or ActiveCampaign, customer records and order history need to flow across for segmentation and follow-up. Most marketing platforms have solid native Shopify integrations.

Where it gets complex: if you’re selling both online and offline, or B2B and B2C, your CRM needs to consolidate customer records across channels without creating duplicates.

Fulfilment and Logistics

Orders need to reach your warehouse or 3PL, get picked, packed, shipped, and tracked. Many Australian businesses use local 3PLs or manage their own warehouse, requiring custom integration to push orders out, receive tracking numbers back, and update Shopify order status.

The Multi-Channel Problem

If Shopify is your only sales channel, integration is relatively straightforward. But most growing e-commerce businesses sell across Shopify, Amazon, eBay, or a wholesale portal — and that’s where complexity escalates.

Inventory across channels: a sale on Amazon needs to reduce stock on Shopify and eBay simultaneously. Without real-time sync, you oversell — damaging marketplace rankings and customer trust.

Order routing: different channels may need different fulfilment workflows. Shopify DTC orders ship via Australia Post. Wholesale orders go through a different process. Marketplace orders have specific packaging requirements.

Unified customer view: without integration, a customer who buys from both Shopify and Amazon is two separate records. You lose the ability to see total customer value or personalise communication.

When Shopify Apps Aren’t Enough

Shopify’s App Store is massive, and for many needs, there’s a plugin that works. But apps have inherent limitations.

Each app is its own silo. Your inventory app doesn’t coordinate with your accounting app. When you have five apps independently syncing data, conflicts multiply.

Apps control the data flow — you don’t. When an app has a bug, changes its sync logic, or updates pricing, you’re at their mercy.

Apps add up. Five apps at $50-100/month each is $250-500/month — for integrations that still don’t fully match your workflow. At that spend, a custom integration often costs less and does exactly what you need.

Planning a Shopify Integration

Before you start building or buying, map out these decisions:

1. What’s your primary integration pain? Inventory accuracy, accounting sync, fulfilment speed, or customer data? Start with the highest-impact connection.
2. How many channels are you selling through? Multi-channel requires a centralised inventory approach from day one.
3. What’s your order volume? Under 50 orders/day, app store plugins are likely fine. Above that, the gaps become expensive.
4. Are you on Shopify Plus? Plus offers higher API limits and exclusive features that make custom integration more viable.
5. What does your fulfilment look like? Self-fulfilled from a single warehouse is different from multi-warehouse or 3PL.

The businesses that get Shopify integration right stop treating Shopify as an island. Shopify is a sales channel — a very good one — but your inventory, accounting, CRM, and fulfilment are the operational backbone. When those systems share data reliably and in real time, your team stops firefighting stock discrepancies and starts focusing on growth.