If you're running a Shopify store in Australia and your accountant is pushing you to connect your accounting software, you've likely hit the same wall: MYOB or Xero? Both are widely used. Both integrate with Shopify. And the internet is full of opinions that don't quite apply to your situation.
The choice matters more than most merchants realise. Get it wrong and you're spending hours each month reconciling mismatched orders, chasing GST errors before BAS, and wondering why your cash flow numbers don't match your bank account. Get it right and the whole thing runs in the background without anyone having to think about it.
In this guide, we'll break down exactly how MYOB and Xero each integrate with Shopify, what to look for in an ecommerce accounting integration for Australian businesses, and which one is the right fit depending on your size, complexity, and accounting setup.
Before comparing MYOB and Xero, it's worth understanding what a Shopify accounting integration is actually supposed to do - because not all integrations are equal.
A properly built Shopify accounting integration should:
If your current integration doesn't do all of the above, you're likely spending more time on manual cleanup than you should be - regardless of whether you're on MYOB or Xero.
Most Australian ecommerce businesses don't choose their accounting software based on how well it integrates with Shopify. They choose it because their accountant recommended it, or because they've always used it. The integration comes later - and that's when the friction starts.
The wrong integration leads to:
Both MYOB and Xero are widely used by Australian businesses, and both can integrate with Shopify - but the depth, reliability, and configuration of that integration varies significantly depending on which connector you use and how it's set up.
MYOB is the most widely used accounting platform among small-to-medium Australian businesses, particularly those in wholesale, distribution, and manufacturing. It comes in several versions - MYOB AccountRight, MYOB Business, and MYOB Advanced - and each has different integration capabilities.
Xero is cloud-native and has built a reputation for being developer-friendly and easy to connect with third-party platforms. It's the preferred choice for many Australian startups, DTC brands, and businesses with a remote-first finance team.
Rather than declaring one a clear winner, the right choice depends on your specific business situation. Here's a practical decision framework for Australian Shopify merchants.
In both cases, the most important decision isn't which accounting platform you choose - it's which connector you use to link it to Shopify. A poorly configured integration will cause problems regardless of whether you're on MYOB or Xero.
Many Australian businesses try to set up their Shopify accounting integration themselves using an off-the-shelf app. For simple stores with low order volumes, that can work. But if any of the following apply, it's worth speaking to a specialist:
Web Ninja specialises in building ecommerce integrations for Australian businesses - including Shopify-to-MYOB and Shopify-to-Xero connectors that handle real-world complexity. If you're not confident your current setup is working correctly, it's worth getting a second opinion before your next BAS.
Both MYOB and Xero can integrate with Shopify effectively - but the right choice depends on your business complexity, your existing accounting setup, and how you plan to grow. For most straightforward DTC Shopify stores, Xero offers a simpler setup. For businesses with B2B channels, complex inventory, or existing MYOB workflows, MYOB is often the better fit.
The most important thing is making sure your integration is actually working the way you think it is. If you're unsure, Web Ninja's team of Australian ecommerce integration specialists can audit your current setup and build a connector that handles your specific requirements - whether you're on MYOB AccountRight, MYOB Advanced, or Xero.
Ready to get your Shopify store and accounting software talking properly? Summon a Ninja today.
Does Shopify integrate with MYOB?
Yes - but Shopify's native MYOB connection is limited. Most Australian businesses use a third-party connector like the one built by Web Ninja to get reliable, real-time sync between Shopify and MYOB AccountRight, MYOB Business, or MYOB Advanced.
Does Shopify integrate with Xero?
Yes. Xero's cloud-first architecture makes it well-suited to Shopify integration, and there are several connectors available. As with MYOB, the quality of the integration depends on which connector you use and how it's configured.
Can I switch from MYOB to Xero without rebuilding my Shopify integration?
Not directly - switching accounting platforms requires rebuilding your integration. However, if you're working with a specialist like Web Ninja, the process can be managed cleanly to avoid data loss or gaps in your sync history.
How do I know if my Shopify accounting integration is working correctly?
Run a monthly reconciliation: compare your Shopify order totals against the corresponding entries in your accounting software. If the numbers don't match, or if some orders are missing, your integration has a problem worth investigating.
Which is better for Australian GST - MYOB or Xero?
Both handle Australian GST well. MYOB has a slight edge for businesses with complex tax scenarios (e.g., mixed taxable/non-taxable products, BAS reporting). Xero is excellent for straightforward GST scenarios and is often preferred by bookkeepers for its ease of use.