Best Accounting Software for Ecommerce Australia 2026

Last updated: March 2026  ·  Prices verified from official AU vendor sites  ·  Affiliate disclosure

Australian e-commerce sellers have a narrower shortlist than they think. Most accounting software for e-commerce handles the ledger fine. What separates the options is how cleanly sales, fees and refunds flow in from Shopify, Amazon and your payment gateways. The best accounting software for Australian ecommerce businesses is Xero. Its native Shopify, Amazon, eBay, and payment gateway integrations are the most comprehensive of any accounting platform in Australia - and they work without complicated setup. MYOB is a distant second for ecommerce due to fewer integrations and a less capable inventory system for multi-channel selling.

Best accounting software for ecommerce Australia (2026)

Software	Price/mo	Shopify	Amazon	Stripe/PayPal	A2X	Inventory
Xero	From $37	✓ Native	✓ via A2X	✓ Native	✓	Basic (add-ons)
MYOB	From $31.82	✓ Limited	✓ via A2X	✓ Limited	✓	Advanced (AccountRight)
QuickBooks	From $32.72	✓ Native	✓ via A2X	✓ Native	✓	Good (Plus plan)

Why Xero works best for most ecommerce businesses

Shopify integration

Xero's native Shopify integration is the strongest in the market. It syncs orders, payments, refunds, fees, and payouts automatically - every sale hits your Xero reconciliation feed correctly coded with no manual entry. The integration handles multi-currency, discount codes, and multiple payment methods. For a growing Shopify store, this saves hours per month on bookkeeping.

A2X for Amazon and eBay

A2X is the standard tool for reconciling Amazon and eBay settlements in Australian accounting software. It connects to Xero natively and breaks down each settlement payout - sales, refunds, fees, advertising costs - and posts them to Xero correctly. Without A2X, reconciling Amazon settlements manually is painful because of how Amazon batches payments. If you sell on multiple channels, A2X + Xero is the most reliable setup.

Payment gateway integrations

Stripe, PayPal, Square, AfterPay, Zip - all have native Xero integrations that automatically reconcile payments and fees. For an ecommerce business processing hundreds of transactions per month, automated reconciliation is essential. MYOB's payment gateway integrations are fewer and less reliable.

Inventory add-ons

Xero's built-in inventory is basic - fine for simple product catalogues, not for multi-warehouse or complex stock management. For growing ecommerce businesses, the standard add-on is Cin7 Omni (formerly Cin7 Core) or DEAR Inventory, both of which connect natively to Xero and handle multi-channel inventory across Shopify, Amazon, eBay, and your warehouse.

What separates good ecommerce accounting software from the rest is not the ledger. It is whether the platform can take a daily payout from Shopify, Amazon or eBay, split out the GST, the merchant fees and the refunds, and land each piece against the right account without you touching it. Get that wrong and you spend every BAS quarter unpicking a single lump sum. That is why the integration matters more here than the accounting features do.

Recommended ecommerce tech stack (Xero)

Function	Tool	Cost
Accounting	Xero (Ignite or Grow)	$37-$78/mo
Shopify reconciliation	Xero native integration	Included
Amazon/eBay reconciliation	A2X	From ~$19/mo USD
Inventory (simple)	Xero built-in	Included
Inventory (advanced)	Cin7 Core or DEAR	From ~$349/mo
Receipt capture	Dext or Hubdoc (included)	Included or from $25/mo
Payroll	Included in Xero	Included

When MYOB might be right for ecommerce

MYOB AccountRight becomes relevant for ecommerce businesses where inventory management is genuinely complex - multiple warehouses, product assemblies (kitting), serial number tracking, or a significant wholesale component alongside direct-to-consumer. At that scale, MYOB's native inventory depth is worth the trade-off in integration complexity. For most ecommerce businesses under $2M annual revenue, Xero plus appropriate add-ons is the right setup.

GST and international sales

Australian ecommerce businesses selling internationally need to know: goods exported from Australia are GST-free; overseas customers buying from you may have GST obligations depending on location and order value; and multi-currency selling requires Xero Comprehensive ($107/mo) or MYOB AccountRight Premier ($190.91/mo). For businesses selling primarily to Australian customers, Xero Ignite ($37) or Grow ($78) handles everything correctly.

Common questions

See also: Best accounting software AU · Xero pricing · MYOB vs Xero

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