Ecommerce Accounting in Australia: GST Thresholds, Stock, Platform Payouts and When to Outsource

Last updated: 13 November 2026. Written by the FreeMyCloud team.

Checked against the Federal Register of Legislation pages for the GST Act, the GST Regulations 2019 and the Corporations Act 2001, ASIC’s company record keeping page and Xero’s own Shopify integration page on 13 November 2026.

Ecommerce accounting is where a lot of well run online businesses quietly come undone. The store reports one revenue figure, the gateway deposits another, and the marketplace takes its fees before the money lands. This guide covers the GST registration turnover threshold, GST on imported goods and overseas sales, stock and margin, how platform payouts should be recorded, what records you have to keep, and where an outsourced bookkeeper fits in.

What does ecommerce accounting actually involve for an Australian online store?

Ecommerce accounting is the same set of jobs any Australian business has: record the income and the costs, reconcile the bank, keep the GST right, and produce numbers the owner can act on. What changes is the shape of the data: a store platform, one or more gateways, possibly two or three marketplaces, a freight provider, advertising billed in another currency, and stock that has to be valued at period end.

That creates three jobs a shopfront does not have. Payouts have to be split, because the money arriving in the bank is net and the gross sale, the fees, the refund and the chargeback belong in different accounts. Stock has to be tracked, because profit on an order means nothing until the cost of the item sold is matched to it. And goods crossing a border have their own GST rules. Everything else is the normal cycle described in our guide to what a bookkeeper does in an Australian small business.

When does an online seller have to register for GST, and what is the GST registration threshold?

The GST registration threshold is $75,000. Section 23-15 of the A New Tax System (Goods and Services Tax) Act 1999 sets a base figure of $50,000 and lets the regulations specify a higher amount, and regulation 23-15.01 of the GST Regulations 2019 specifies $75,000. For a non-profit body, regulation 23-15.02 specifies $150,000. Both are current in the compilation in force from 1 November 2025. Registration must be applied for within 21 days of becoming required to register, under section 25-1 of the GST Act.

The test is GST turnover, not profit and not what reaches the bank. A store selling $90,000 through a marketplace might see only $70,000 of deposits after fees and refunds, so it can be required to register while the bank balance suggests otherwise. The channel makes no difference. Our posts on BAS lodgement and the BAS and the ATO page cover that side. FreeMyCloud is not a registered tax or BAS agent and does not lodge, so prepared figures go to your own registered agent.

How does GST on imported goods work, and are overseas sales GST-free?

GST on imported goods splits into two regimes. Under section 84-79(3) of the GST Act, goods are low value goods if their customs value is $1,000 or less and they are not tobacco, tobacco products or alcoholic beverages. For those the GST is generally collected by the seller rather than at the border: section 84-77 catches overseas suppliers who arrange delivery into Australia, sales made through an electronic distribution platform, and goods brought in by a redeliverer, and section 84-81 treats the platform operator or redeliverer as the supplier. Consignments above $1,000 are taxed as a taxable importation at the border instead.

Selling overseas is not automatically GST-free either. Item 1 of the table in section 38-185 makes a supply of goods GST-free only if the supplier exports them before, or within 60 days after, the earlier of receiving any payment and issuing the invoice, unless the Commissioner allows longer. A pre-order paid in March and shipped in June does not meet that test on its face.

So two purchases from the same supplier can carry GST in different places: one on the invoice, one on a clearance document weeks later, and a third not at all. Coding all three the same way is a common error in an online retailer’s file.

How do you handle inventory accounting and cost of goods sold in an online business?

Inventory accounting is the difference between knowing your margin and guessing it. Cost of goods sold is the cost of the items actually sold in a period, and until it is recorded against the matching sales a profit and loss report is close to meaningless. A store can post a strong revenue month and go backwards, and the owner will not see it until the next container has to be paid for.

Two things make this harder online. The cost of a unit is rarely just the supplier price, because freight, duty, clearance and warehouse handling all belong in the landed cost. And stock sits in several places at once, so a quantity in the software is only as good as the last count behind it.

The usual approach is to keep detailed stock records in the platform or a dedicated inventory system, post a periodic cost of goods sold journal to the ledger, reconcile the two monthly and count once a year. The reporting that follows is what our business reports service is built around.

What does ecommerce bookkeeping look like week to week?

Ecommerce bookkeeping is mostly a rhythm. The transactions arrive automatically, so the work is checking that what the platform says happened matches what the bank says happened, and that the GST and the stock moved with it. Done weekly it takes a couple of hours. Left for a quarter it becomes a reconstruction job.

The cycle below is deliberately boring. The value is in it happening on the same day every week.

The money in and money out side sits in our accounts receivable and payable and debtors management services, and in our posts on accounts payable outsourcing and unpaid invoices.

How does a Shopify Xero integration handle payouts and fees?

A Shopify Xero integration exists because the payout problem is tedious by hand. On its own Shopify integration page, Xero says the integration brings Shopify sales into Xero either as a daily summary or as individual sales for each payment gateway, automatically matches payouts from Shopify Payments and other gateways to the bank account with fees, refunds and taxes handled, and shows online store and point of sale fees together in the dashboard.

That solves the mechanics, not the judgement. A connector posts what it is configured to post, so the tax rates, clearing accounts and the treatment of refunds and gift cards have to be mapped correctly once, by someone who knows what the GST answer should be. Get it wrong and the file produces a consistent, incorrect BAS figure every quarter.

If the ledger itself is the piece you want handled, see our Xero bookkeeping services and MYOB bookkeeping services pages, or our comparison of the best accounting software in Australia.

What records does an online business have to keep, and for how long?

Two retention periods matter most. If the business is a company, section 286 of the Corporations Act 2001 requires written financial records that correctly record and explain its transactions and financial position and performance, and subsection 286(2) requires them to be retained for seven years. ASIC’s own company record keeping page says the same plainly: at least seven years, electronic records are fine provided hard copies can be produced within a reasonable timeframe, and directors can access the books at all reasonable times.

The second is the GST clock. Section 93-5 of the GST Act ends the entitlement to a GST credit on a purchase not taken into account within four years after the day the return for that tax period was due. For a store with steady stock and freight purchases, an unfinished year of coding is real money attached to a deadline.

When is outsourced bookkeeping the right fit for an online business, and when is it not?

Outsourced bookkeeping suits an online store when the work is steady, rules based and repeatable, which describes most of the weekly cycle above, particularly when volume has outgrown what the owner can do on a Sunday night. FreeMyCloud has placed university-qualified graduate accountants based in the Philippines with Australian businesses since 2010, working in the client’s own software during Australian business hours, at about 50% less than employing a bookkeeper locally. Our bookkeeping for online businesses page sets out what that covers for a store, and the how it works page walks through the arrangement.

It is not right for everything. If the real problem is stock and warehouse process rather than bookkeeping, fix that first, and a pre revenue store doing a handful of orders a month needs a few hours with its accountant, not a bookkeeper. If nobody internally can approve a payment or answer a question about an odd order, outsourcing will stall, because the provider does the work while the owner keeps the decisions.

Only a registered BAS or tax agent can provide BAS services for a fee, so that split is legal as well as practical, as our post on who does what between a bookkeeper, a BAS agent and an accountant explains. Data access is covered in offshore bookkeeping and data security, the models available here in our review of outsourced bookkeeping services in Australia, and the rest in the outsourced bookkeeping FAQs. There are no lock-in contracts and no setup fees, and FreeMyCloud works with clients from individual operators to ASX-listed companies.

Frequently asked questions

How is Shopify accounting different from accounting for a shopfront?

Shopify accounting differs mainly in how the money arrives. A shopfront banks its takings; a Shopify store receives a net payout after platform and gateway fees, refunds and chargebacks. Xero’s own Shopify integration page describes bringing sales in as a daily summary or as individual sales per gateway and matching payouts to the bank. The second difference is stock, which has to be valued and journalled rather than counted at a till.

Do you need an ecommerce accountant, an ecommerce bookkeeper, or both?

Most growing stores use both. An ecommerce bookkeeper keeps the ledger current week to week: payouts reconciled, stock journals posted, GST coded, BAS figures prepared, reports out monthly. An ecommerce accountant works at a lower frequency and a higher altitude on structure, tax position, year end statements and lodgement. Using the accountant for the weekly bookkeeping works, but it is expensive and the numbers end up accurate only once a quarter.

Which ecommerce accounting software suits an Australian online store?

Xero, MYOB, QuickBooks and Reckon will all handle an online store, and all connect to the major platforms natively or through a connector, so the setup matters more than the badge. What does change the decision is stock complexity: a few dozen lines can usually sit inside the accounting package, while hundreds of lines or several warehouses normally need a dedicated inventory system feeding summary journals into the ledger.

What do ecommerce accounting services and ecommerce bookkeeping services usually cover?

Ecommerce accounting services and ecommerce bookkeeping services usually cover payout and gateway reconciliation, coding of freight, advertising and app costs, the GST treatment of imports and exports, cost of goods sold journals, stock reconciliation, accounts payable and receivable, monthly management reports, and preparing the figures a registered BAS agent needs. Lodgement, tax planning and year end statements sit with your registered agent.

Is accounting for ecommerce different from accounting for a normal retail business?

Accounting for ecommerce uses the same standards and the same GST law as any retailer. What differs is the data: multiple sales channels, net settlements instead of daily banking, foreign currency costs, and stock spread across a warehouse, transit and a fulfilment provider. The obligations are identical. The reconciliation work is heavier, and it goes wrong faster if it is left for a quarter.

How long do I have to claim GST credits on stock and platform fees?

Four years. Section 93-5 of the GST Act says you cease to be entitled to a GST credit for a purchase to the extent it has not been taken into account within four years after the day the GST return for the relevant tax period was due. For a store with regular stock, freight and platform fee purchases, an unfinished year of coding can become permanently unclaimable.

This article is general information about Australian bookkeeping and reporting obligations, current as at 13 November 2026. It is not tax, financial or legal advice. FreeMyCloud is not a registered tax or BAS agent and does not prepare or lodge tax returns or business activity statements. Rates, thresholds and dates change. Confirm your own position with your registered tax or BAS agent.