An online business is not “a small business with a different shopfront.” It is a business with multi-channel sales, payment processor settlements, foreign-currency receipts, platform fees that change every time a marketplace updates its terms, and a much higher transaction volume per dollar of revenue than almost any bricks-and-mortar equivalent.

Which is why generic small-business accounting often falls over when the client is an Australian e-commerce seller. The bookkeeping is fine. The compliance is fine. But the GST treatment of marketplace fees is wrong, the Shopify settlement is reconciled to “Sales” instead of broken into its components, and nobody noticed that the foreign-currency Stripe receipts are sitting in the wrong account.

This guide explains what an Australian online business actually needs from its accountant in 2026 — covering Shopify, Amazon, eBay, Etsy, Squarespace and other platforms — and what to look for when you’re shopping for one. It comes from our team at Trinity Accounting Practice — a Sydney-based registered tax agent practice that works with online sellers across Australia.

Why Online Business Accounting Is Different

Five things separate an e-commerce file from a typical small-business file:

Settlement vs sales. Shopify, Amazon and similar platforms don’t deposit gross sales into your bank account. They deposit net of platform fees, payment processing fees, refunds, chargebacks, and sometimes tax withheld. Reconciling to the bank deposit alone misses everything in between.
Marketplace GST. Some platforms now collect and remit GST on your behalf for certain transactions (low-value imports, for instance). The income should still be reported correctly — and the GST treatment is not always obvious.
Foreign currency. Stripe in USD, PayPal in multiple currencies, Amazon US sales — all need to be converted to AUD using the correct date, and foreign-currency gains/losses recorded.
Inventory. If you hold stock, your COGS calculation needs to reflect what was actually sold in the period, not what was purchased. Inventory systems that talk to Xero (Cin7, DEAR, Unleashed, Katana) are usually the right approach.
Transaction volume. A bricks-and-mortar retailer might have 500 transactions a month; an online seller in growth mode can have 5,000. Manual handling stops working very quickly.

What a Good Online Business Accountant Should Handle

Beyond the standard tax compliance (BAS, IAS, annual return), an e-commerce accountant should be comfortable with:

Platform → accounting integration. A2X for Shopify/Amazon, Link My Books for Etsy/eBay, or direct API connections — these tools translate settlement deposits into proper sales, fees, refunds and tax lines in Xero.
Multi-currency setup in Xero. Including correct base currency, FX revaluation, and FX gain/loss reporting.
Sales tax across jurisdictions. For Australian sellers exporting to the US, EU or UK — registration thresholds, marketplace facilitator rules, and how to report the income for Australian GST purposes.
Inventory accounting. Periodic vs perpetual, FIFO vs average cost, year-end count process. Most generalists are uncomfortable with inventory — it’s a specialist skill.
Cash flow forecasting for inventory-heavy businesses. Cash is tied up in stock for weeks before it sells, and growth often means cash going backwards before it goes forwards. A good e-commerce accountant understands this rhythm.
Marketplace fee analysis. Knowing the difference between Amazon FBA fees (and which are deductible), Shopify subscription vs transaction fees, and how PayPal cross-border fees show up.

Platform-Specific Notes

Shopify

Shopify Payments deposits net of processing fees and any chargebacks. Without a tool like A2X, the bookkeeper sees a single net deposit and has no easy way to break it into gross sales, processing fees, refunds and tax. The result is usually under-reported revenue and over-reported margin — which then catches up at tax time.

Amazon

Amazon is the most complex of the big platforms. FBA fees, storage fees, advertising spend, refunds, multi-marketplace activity (AU + US + UK), and Amazon-collected GST on certain transactions all need to flow into Xero correctly. A2X for Amazon is generally non-negotiable above $250k in Amazon sales.

eBay

eBay now processes payments directly (rather than via PayPal as it once did). Fees are deducted at settlement, so the same settlement-vs-sales issue exists. The eBay Australia reporting has improved markedly in recent years, but most generalists still don’t reconcile it properly.

Etsy

Etsy reports in AUD for Australian sellers, but charges a mix of listing fees, transaction fees, payment processing fees and advertising spend. Each is a different deductible category.

Squarespace, Wix, BigCommerce

Generally simpler than the marketplaces because you control the checkout. The complication shifts to your payment processor (Stripe, Square, PayPal) settlement timing.

The Questions to Ask Any Accountant Before Engaging Them

“Do you currently have other e-commerce clients?” Specifics matter. “I have a couple of Shopify clients” is good. “I work with retail businesses” is not the same thing.
“How do you handle the Shopify / Amazon settlement reconciliation?” The answer should mention A2X, Link My Books, Bookkeep, or a documented manual process. A blank look here is a warning sign.
“How do you handle foreign currency in Xero?” Multi-currency Xero, monthly FX revaluation, and dedicated FX gain/loss accounts should be in the answer.
“How do you advise on inventory?” Cost flow method (FIFO/average), year-end count process, and an opinion on the right inventory app for your scale.
“What’s your view on the GST treatment of overseas sales?” The answer should be specific — GST-free exports vs out-of-scope, and the documentation required to support the export classification.

The Common Mistakes We Untangle for New E-commerce Clients

Settlement deposits coded entirely to “Sales.” The fees, refunds and chargebacks are buried inside — distorting revenue and obscuring margin.
GST claimed on Stripe / PayPal fees. These are GST-free supplies of financial services. Common mistake.
Foreign-currency receipts left in AUD-equivalent without FX revaluation. Realised and unrealised FX gains/losses are often missing entirely.
Inventory written down to whatever the year-end count says, without journal documentation. Auditors and lenders ask. Be ready.
Amazon advertising spend treated as a different category to other marketing. Sometimes deductible immediately, sometimes capitalised — depends on what the spend produced.

A Trinity insight from 22 years in practice

The single biggest improvement most growing e-commerce businesses can make has nothing to do with tax. It is forecasting cash flow against the inventory cycle. We’ve watched profitable online sellers run out of cash because every dollar of profit was tied up in next month’s shipping container — and they had no model showing them when the squeeze was coming. A 30/60/90 cash forecast updated monthly is worth more to a growing online seller than almost any tax-planning strategy.

What This Means for You

If your accountant doesn’t ask about Shopify settlement breakdowns: they are not an e-commerce accountant. They are a generalist with an e-commerce client.
If you sell on multiple platforms: get the integration tools right before you scale. Re-categorising 18 months of transactions retrospectively is painful and expensive.
If you sell overseas: get sales tax classification right early. The US sales tax landscape in particular is a maze, and the wrong assumption can compound quickly.

How Trinity Can Help

Trinity Accounting Practice works with online businesses across Australia — Shopify, Amazon, eBay, Etsy, Squarespace, and custom-built stores. We can review your existing Xero setup, recommend the right integration tools, manage the monthly settlement reconciliation, model your cash flow against inventory cycles, and handle the full tax and BAS compliance. As a registered tax agent firm with Certified Xero Advisors, we have the credentials and the e-commerce specialism in one place.

Book a 30-minute e-commerce accounting review with the Trinity team →

General advice only. This article contains general information current as at May 2026 and does not constitute tax, financial or legal advice. It does not take into account your personal circumstances, objectives, or needs. Marketplace facilitator rules, GST thresholds, and overseas sales tax obligations change — always verify current rules on ato.gov.au and with appropriate overseas advisers. Before acting on any information in this article, you should consider its appropriateness to your situation and seek professional advice from Trinity Accounting Practice or another qualified adviser.