Ecommerce Accounting Software: The Australian Seller’s Stack

Reviewed by Reuben Bergola, CA, Managing Partner, New Wave Accounting. Last reviewed 27 October 2026.

The best ecommerce accounting software is not one program but a stack: a general ledger (Xero, MYOB or QuickBooks Online), a settlement tool that turns Shopify, Amazon and eBay payouts into clean summaries, and an inventory system that gives you real cost of goods sold. Get those layers right and your BAS, margins and monthly reports start to make sense.

Below we explain each layer, compare the three main ledgers and suggest a stack for each stage of growth. For the bigger picture, start with our complete guide to ecommerce accounting.

The six layers of an ecommerce accounting stack

Each layer does one job and hands clean data to the next.

General ledger

Your system of record. It must handle Australian GST, lodge your BAS (Business Activity Statement, the form you use to report and pay GST and PAYG withholding to the ATO) and run payroll that reports through Single Touch Payroll.

Settlement connector

A Shopify or Amazon payout is not one sale. It bundles orders, refunds, fees and other charges into one net deposit. A connector such as A2X reads that payout and posts one summary that “covers the exact period you are paid for”, so it reconciles cleanly to the bank deposit. A2X currently lists Shopify, Amazon, eBay, Etsy, Walmart, TikTok Shop and PayPal as sources, and Xero, QuickBooks Online, Sage and NetSuite as destinations. See our Shopify and Xero integration guide and Amazon seller accounting guide for setup detail.

Inventory management

Cost of goods sold (COGS) is what the stock you actually sold cost you. Without inventory tracking, your ledger treats every stock purchase as an expense the day you buy it, so margins swing wildly month to month. Landed cost (the product price plus freight, duty and other costs to get it to your warehouse) belongs in that unit cost too. Our inventory and landed cost guide covers this in depth.

Receipts and reporting

Receipts capture keeps supplier bills and GST evidence attached to each transaction, which matters because the ATO generally requires most business records to be kept for five years. Reporting is the payoff: margin by channel, cash runway and a BAS you trust.

Xero vs MYOB vs QuickBooks for Australian online sellers

All three ledgers handle Australian GST and BAS. The real differences for ecommerce are how well they connect to your sales channels, how they handle inventory and whether multi-currency is on the plan you are paying for. The table lists only features we confirmed on each vendor’s official site in October 2026. Plans change often, so we have left prices out. Check current pricing pages before you choose.

Worth noting:

• Inventory costing differs. Xero uses weighted average cost. QuickBooks Online uses FIFO, treating the first items you buy as the first you sell. Neither is wrong, but be consistent.
• Xero’s built-in inventory has limits. Xero itself suggests a third-party app if you need “multi-location tracking, batch or serial numbers.”
• MYOB’s ecommerce path is narrower. Shopify connects through Amaka, which can sync sales, daily inventory adjustments and a daily COGS journal. A2X does not currently list MYOB.

Being upfront about our bias

New Wave Accounting is a Xero Platinum Partner and A2X certified, so most of our ecommerce clients run Xero with A2X. That reflects the app ecosystem, not a claim the others cannot work. If MYOB or QuickBooks is already set up well for you, switching is not always worth the disruption. See our Xero accountant services for how we work in Xero.

When to add a dedicated inventory app

Built-in ledger inventory is fine for a simple catalogue. Consider a dedicated inventory or order management app when:

• You hold stock in more than one location (say, a 3PL plus Amazon FBA).
• You need batch, expiry or serial number tracking.
• You assemble kits or bundles, or manufacture.
• You need to spread freight and duty across each shipment to get a true landed cost per unit.
• Your SKU count is approaching your ledger’s limit (4,000 tracked items in Xero).

The Xero App Store inventory category lists options such as Cin7 Core, Unleashed Software and Katana Cloud Inventory. When you add one, decide which system owns inventory value and posts COGS. Two systems both posting COGS (or two connectors both posting sales) is a common way to double count.

A suggested stack by stage

General guidance only. Your channels and product type matter more than revenue alone.

Starting out (one store, under about $500K)

• Ledger with GST and BAS lodgement.
• One connector: Xero’s free Shopify integration on daily summary, or A2X if you also sell on Amazon or eBay.
• A simple SKU cost list so you can calculate COGS at least monthly.
• Receipts capture switched on from day one.

Growing ($500K to $2M, often two or three channels)

• Xero (or your existing ledger) plus A2X for each channel, with COGS posted from your SKU costs.
• A separate clearing account for each payment gateway (more on this below).
• Monthly inventory counts or reconciliation, and a monthly margin report by channel.
• Payroll that reports through STP. From 1 July 2026, the ATO says STP reports must also include qualifying earnings and super liability under Payday Super, so check your payroll software is updated.
• Proper ecommerce bookkeeping rather than catching up at BAS time.

Scaling ($2M+, multi-channel)

• A dedicated inventory or order management app as the source of truth for stock and landed cost.
• A2X for marketplace and store settlements, split by channel and tax treatment.
• Multi-currency enabled if you buy or sell offshore.
• Management reporting: KPI dashboards, cash flow forecasting and margin by product line.
• An accountant who reviews the whole stack, not just year-end numbers, such as our ecommerce accountant team.

Common mistakes that break the numbers

Syncing every order into the ledger

Posting each order as an invoice floods your ledger with transactions that never line up neatly with a payout. Even Xero suggests its daily summary option for high-volume stores.

No clearing account

A clearing account is a holding account in your ledger. The connector posts the expected payout into it, the bank deposit is matched against it, and the balance should come back to zero. A leftover balance flags something missing, often gateway fees. A2X’s guides use this approach for gateways like PayPal and Zip that deduct fees before paying out.

No inventory tracking

If stock purchases go straight to an expense account, a big stock order makes a profitable month look like a loss and the next month look brilliant. It is one of the profit leaks we see most often.

Getting GST on fees and overseas sales wrong

In Australia, Shopify adds tax to its processing fees, so those fees carry GST you may be able to claim. Overseas sales can be treated differently again, so map tax rates carefully in the connector. Our GST guide for online sellers explains the rules.

A real example

One of our clients, an online retailer selling internationally, came to us because their margins did not add up. We connected A2X to Xero, rebuilt the chart of accounts, set up monthly inventory tracking and corrected the GST treatment. The owner now gets reliable monthly figures and accurate margins.

FAQ

What is the best accounting software for ecommerce in Australia?

There is no single best option. Xero, MYOB and QuickBooks Online all handle Australian GST, BAS and Single Touch Payroll. For multi-channel sellers, the deciding factor is usually which settlement and inventory apps connect to the ledger. A2X, for example, supports Xero and QuickBooks Online but does not list MYOB.

Is Xero good for ecommerce?

For many sellers, yes. It has a free native Shopify integration, A2X support and a large App Store. Its built-in inventory suits a single location with up to 4,000 tracked items. Beyond that, you would usually add a dedicated inventory app.

Do I need A2X if I already use Xero’s Shopify integration?

Not always. If you only sell through Shopify, the native integration on daily summary can be enough. A2X becomes more useful when you sell on several channels such as Amazon, eBay or Etsy, want COGS posted automatically, or need settlements split by tax treatment and channel.

Can QuickBooks Online track inventory for an online store?

Yes, on the Plus and Advanced plans. It uses FIFO costing. If you need multiple warehouses or landed cost allocation, you would typically add a dedicated inventory app.

Does MYOB work with Shopify?

Yes. MYOB Business connects to Shopify through Amaka, which can sync sales, inventory adjustments and a daily COGS journal. MYOB says Business Pro is needed to see sales orders sent from third parties.

Should I switch accounting software as my business grows?

Only if your current ledger cannot connect to the tools you need, such as multi-currency or your marketplace connectors. A messy setup usually stays messy in a new ledger. Fix the chart of accounts, clearing accounts and inventory process first.

Talk to an ecommerce accountant

If your stack has grown piece by piece and the numbers no longer reconcile, we can review it and tell you what to keep, change or switch off. New Wave Accounting is a Chartered Accounting firm, registered tax agent (25483393), Xero Platinum Partner and A2X certified, working with online sellers across Australia. Learn more about our ecommerce accountant services or book a free 20-minute call.

This is general information only and does not consider your circumstances. Talk to a registered tax agent before acting on it.

Sources

• Xero AU pricing and plans: https://www.xero.com/au/pricing-plans/
• Xero AU multi-currency: https://www.xero.com/au/accounting-software/use-multiple-currencies/
• Xero AU inventory management guide (4,000 tracked items, weighted average cost, app suggestions): https://www.xero.com/au/guides/inventory-management-system/
• Xero STP Phase 2: https://www.xero.com/au/programme/single-touch-payroll/stp-2/
• Xero App Store AU, Shopify integration by Xero: https://apps.xero.com/au/app/shopify
• Xero App Store AU, inventory category: https://apps.xero.com/au/function/inventory
• MYOB AU pricing: https://www.myob.com/au/pricing
• MYOB support, connect Shopify to MYOB (Amaka): https://www.myob.com/au/support/myob-business/inventory/connect-your-shopify-account-to-myob
• QuickBooks AU pricing: https://quickbooks.intuit.com/au/pricing/
• QuickBooks AU help, set up and track inventory: https://quickbooks.intuit.com/learn-support/en-au/help-article/stock-management/set-track-inventory-quickbooks-online/L22FZLBGN_AU_en_AU
• QuickBooks AU payroll: https://quickbooks.intuit.com/au/payroll/
• A2X integrations: https://www.a2xaccounting.com/integrations
• A2X support, connect to your accounting system: https://support.a2xaccounting.com/en/articles/5920731-connect-a2x-to-your-accounting-system
• A2X for Shopify: https://www.a2xaccounting.com/shopify
• A2X support, Shopify and ZipPay clearing account example: https://support.a2xaccounting.com/en/articles/3771441-a2x-for-shopify-and-zippay-reconciling-payouts-and-accounting-for-zippay-fees-monthly
• A2X, reconcile PayPal for Shopify: https://www.a2xaccounting.com/ecommerce-accounting-hub/reconcile-paypal-shopify-a2x
• Shopify Help, pay periods and fees (tax added to fees in Australia): https://help.shopify.com/en/manual/payments/shopify-payments/payouts/pay-periods-and-fees
• ATO, Single Touch Payroll: https://www.ato.gov.au/businesses-and-organisations/hiring-and-paying-your-workers/single-touch-payroll
• ATO, STP reporting under Payday Super: https://www.ato.gov.au/businesses-and-organisations/super-for-employers/paying-super-on-payday/single-touch-payroll-reporting-under-payday-super
• ATO, overview of record-keeping rules for business: https://www.ato.gov.au/businesses-and-organisations/preparing-lodging-and-paying/record-keeping-for-business/overview-of-record-keeping-rules-for-business