Connecting Shopify to MYOB or Xero: What Each Integration Actually Syncs

Shopify integrates with both Xero and MYOB, and for most Australian stores the connection is an app, not a project. The choice that matters is not really which app. It is what lands in your ledger: one invoice per order, or a summary per day or per payout. Choose badly and your bookkeeper spends each month matching hundreds of invoices to a few deposits.

Here is what each option actually syncs, how GST comes through, and where MYOB’s product line changes the answer. Prices were checked on 1 October 2026 on each vendor’s own pages.

Start with how Shopify pays you

A Shopify Payments payout is not one order. It is the balance of everything charged over the period, less processing fees, less refunds, which Shopify deducts from your next available payout. You can choose a daily, weekly or monthly payout schedule. In Australia, payments captured on Friday, Saturday and Sunday are combined into a single payout.

So one line on your bank statement can stand for dozens or hundreds of orders, net of fees. Every integration has to answer the same question: how does that one deposit get matched to the sales behind it?

Per-order invoices or summaries

There are three ways to post Shopify sales into accounting software:

• Per order. Every order becomes its own invoice, with the customer and line items.
• Daily summary. One invoice holds a day’s sales, split by account and tax rate.
• Per payout. One entry covers everything inside a payout, so it matches the bank deposit.

Per-order sync suits low volumes, or wholesale where you need receivables by customer. As volume grows it makes a mess: hundreds of invoices a week to match against a few lumped deposits, fees to split back out, and refunds that come out of a later payout than the sale they reverse. Xero’s own listing agrees: a daily summary for high-volume stores, per-sale transactions when you need customer and line-item detail.

With a summary, order detail stays in Shopify, where you would look it up anyway.

Option 1: Shopify integration by Xero

Xero has its own Shopify integration. Xero says it syncs sales, payouts, fees and taxes, as a daily summary or as individual sales, and matches payouts from Shopify Payments and other gateways to your bank account, with fees, refunds and taxes handled. It can sync up to 90 days of historical data. Xero lists it as free on all Xero plans, and has partnered with Amaka to help with setup.

Its listing does not mention inventory, so treat it as a sales and payouts sync, not a stock sync.

Option 2: A2X, for payout-level reconciliation

A2X takes the per-payout approach. Rather than pushing individual orders into Xero, it posts one summary per payout, matched to the deposit, with sales, fees, taxes, refunds and gift cards categorised. In Xero the payout arrives as a draft invoice, or a draft bill if the payout is negative, so you can review it before it reaches the books.

A2X’s Shopify pricing is in US dollars: Mini at US$29 a month for up to 200 orders a month, Basic at US$45 for up to 500, and Professional at US$79 for up to 2,000, with higher tiers above that and a 30-day free trial.

One limit for MYOB users: A2X’s Shopify App Store listing names QuickBooks Online, Xero, Sage and NetSuite. MYOB is not on the list.

Option 3: Amaka, the usual route for MYOB

MYOB’s own help centre documents connecting Shopify to MYOB Business through Amaka. It syncs daily, and you choose whether the day’s transactions go in as a single summarised invoice or as separate invoices per transaction, optionally split by location. Third-party fees are created as bills. Inventory is adjusted daily for Shopify sales and refunds, and cost of goods sold goes in as a daily journal.

Amaka also connects Shopify to Xero and QuickBooks Online. Its Shopify App Store pricing, billed in US dollars, has a free plan for up to 60 orders a month on one store, Premium at US$18 a month (or US$156 a year) for up to 500 orders a month across two stores, and Premium+ at US$49 a month (or US$468 a year) with unlimited orders.

Which MYOB you have changes the answer

“MYOB” covers several different products, and the Shopify options depend on which you run.

• MYOB Business Lite and Pro run in the browser. AccountRight Plus and Premier are now sold under the MYOB Business name as well, and run on Windows desktop and in the browser. MYOB’s marketplace lists the Amaka integration as working with AccountRight, MYOB Business and MYOB Essentials.
• MYOB Acumatica, formerly MYOB Advanced, is MYOB’s cloud ERP for mid-sized businesses. MYOB’s marketplace lists a Shopify for MYOB Acumatica app, and asks existing Acumatica customers to contact MYOB’s enterprise team to connect it.
• MYOB Exo is MYOB’s on-premise business management software. The Shopify options on MYOB’s marketplace for Exo are third-party connectors, such as CyberWorkshop’s Shopify sync for MYOB EXO and Web Ninja’s connector, which syncs products, pricing and stock from MYOB to Shopify and sends orders back.

The Exo and Acumatica connectors move orders, stock, pricing and customers between Shopify and an ERP. That is closer to an ERP integration than an accounting sync, and they should be scoped like one.

GST for Australian merchants

Four GST details catch Australian stores out, whichever tool you use.

• Prices. Australian customers expect prices to include tax, and Shopify has a setting to include tax in product prices and shipping rates. The integration then has to separate the GST from each sale.
• Tax mapping. Shopify’s tax lines need mapping to your GST codes. MYOB’s guide to the Amaka integration asks you to map Shopify taxes to MYOB tax codes, and A2X lets you set tax rules for each transaction type. GST-free products are where the mapping usually goes wrong; we covered those carve-outs in GST and shipping for Australian stores.
• Fees. In Australia, 10% GST is included in all Shopify Payments processing fees. Shopify issues a monthly invoice showing the GST paid on those fees, on the 5th of the following month. Check that your integration posts fees to a tax code that carries that GST.
• Shopify’s own bill. Shopify charges 10% GST on your subscription and shipping labels unless you are registered for GST and add your ABN to the store.

Run the mapping past your accountant before the first sync, not after the first BAS.

When a custom integration makes sense

For most stores on Xero, MYOB Business or AccountRight, an off-the-shelf app is the right answer, and we would tell you so. A custom integration earns its cost when:

• You run Exo or Acumatica and the marketplace connectors do not map your stock, pricing or customer accounts the way your business works.
• Wholesale customers need account-specific pricing or terms pulled from the ERP into Shopify.
• Orders need to reach a warehouse or fulfilment system with data the standard connectors leave behind.

That usually means a small custom Shopify app or middleware between Shopify and the ERP. Treat it as software you own, because Shopify and the ERP will both change underneath it.

What we would pick

• Xero, modest volume: start with Xero’s own integration, which is free.
• Xero, high volume or several gateways: look at A2X, where one entry per payout matches the bank deposit.
• MYOB Business or AccountRight: Amaka, as documented by MYOB, set to a daily summary unless you need invoices by customer.
• MYOB Exo or Acumatica: treat it as an ERP integration and scope it properly.

Our Shopify-certified developers can help you choose and set up the right one, or build what the apps cannot. More on our Shopify development work.

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Sources: Shopify integration by Xero and its Xero App Store listing, A2X Shopify pricing, A2X on the Shopify App Store, A2X: sending your first invoice or journal, Amaka on the Shopify App Store, MYOB: connect your Shopify account to MYOB, MYOB App Marketplace: Shopify by Amaka, MYOB pricing, MYOB Exo, MYOB Advanced Business is now MYOB Acumatica, and the Shopify Help Center on Australian payouts, refunds and payouts, GST on Shopify Payments fees and GST on Shopify bills.