Online retail looks simple from the outside: sell a product, get paid. The accounts tell a messier story. Revenue arrives as net payouts from five different platforms. Fees are buried in settlement reports. Stock bought from overseas carries freight, duty and GST at the border. Refunds land in a different month from the sale. And the profit and loss shows "sales" without telling you whether the Amazon channel is subsidising the Shopify store or the other way round.
We work with Shopify stores, Amazon and eBay sellers, wholesalers selling online, and bricks-and-mortar retailers with an online channel. Here is what we fix and what we watch.
Why do online sellers so often not know their real margin?
- Payouts recorded as sales. The bank shows one deposit. The platform took fees, refunds, chargebacks and sometimes a reserve before paying. Recording the deposit as revenue understates both sales and costs, and often gets GST wrong.
- No landed cost. The supplier invoice is only part of the cost. Freight, insurance, customs duty, broker fees, inbound 3PL charges and currency movements belong in the cost of each unit.
- Channel costs mixed together. Marketplace commission, fulfilment fees, ad spend and returns differ hugely between channels, but most P&Ls lump them into one line.
- Cash locked in stock. Profit on paper, no cash in the bank, because last quarter's profit is sitting in a warehouse.
- GST on imports done by guesswork. Import GST, overseas supplier invoices and platform fees from offshore companies each have their own rules.
What does an ecommerce accountant do for you?
- Platform reconciliation. Each payout is broken into gross sales, refunds, fees, shipping income, GST and reserves through a clearing account, so the net figure matches the bank to the cent.
- Inventory and cost of goods sold tied to your inventory system, with landed cost calculated per shipment.
- Margin by channel and by product line every month.
- BAS with import GST, overseas supplier invoices and GST-free exports correctly treated.
- Cash flow forecasting around stock orders, peak season and supplier payment terms.
- Tax planning and structure as revenue grows.
How do the main platforms reconcile into Xero?
| Platform | What arrives in the bank | What needs recording separately | Common error |
|---|---|---|---|
| Shopify Payments | Net payout, often several days' orders | Gross sales, refunds, Shopify fees, chargebacks, GST collected | Payout coded as sales |
| Amazon Seller Central | Settlement every two weeks or so | Sales, referral fees, FBA fees, advertising, reimbursements, reserves | Fees netted off sales, so margin looks higher |
| Stripe and PayPal | Net of processing fees, sometimes in foreign currency | Fees, currency conversion, disputes | Foreign currency gains and losses ignored |
| eBay and other marketplaces | Net payout | Final value fees, promoted listing fees, refunds | Refunds recorded in the wrong month |
| Buy now, pay later | Net of merchant fee | Merchant fees as a cost of sale | Fees hidden inside sales |
Our bank statement and transaction list agents convert statements and settlement exports into clean, import-ready files, and our transaction coding agent suggests the account and GST code for each line. A bookkeeper reviews and approves every entry.
Which KPIs matter for an online store?
| KPI | How it's worked out | What it tells you |
|---|---|---|
| Contribution margin per order, by channel | Sale price less landed cost, platform fees, fulfilment, payment fees and returns | Which channel earns money before overheads |
| Gross margin by product line | (Sales less landed cost) ÷ sales | Which products to push, reprice or drop |
| Customer acquisition cost | Marketing spend ÷ new customers | Whether growth is profitable |
| Return on ad spend | Revenue from ads ÷ ad spend | Read it against contribution margin, not gross revenue |
| Stock turns and days of stock | Cost of goods sold ÷ average stock | How long your cash sits on a shelf |
| Refund and return rate | Refunds ÷ gross sales | Product quality, sizing or description problems |
Example: the same product on two channels
Say you sell a $60 (GST-inclusive) product with a landed cost of $18.
| Per unit (ex GST) | Your Shopify store | Amazon with FBA |
|---|---|---|
| Sale price | $54.55 | $54.55 |
| Landed cost | $18.00 | $18.00 |
| Platform and payment fees | $1.90 | $8.20 |
| Fulfilment and postage | $9.50 | $7.40 |
| Ads per sale | $8.00 | $4.00 |
| Returns allowance | $1.50 | $2.50 |
| Contribution margin | $15.65 (29%) | $14.45 (26%) |
The figures are illustrative, but the lesson holds: the channel with higher fees can still be close on margin once ad spend and fulfilment are counted. Without this table, most sellers guess.
What tax and GST rules are specific to ecommerce?
GST on goods you import
- Goods over A$1,000 customs value attract GST at the border when imported, which a registered business can generally claim back as a GST credit in its BAS (ATO guidance for Australian businesses importing). Larger importers can apply to the deferred GST scheme so import GST is reported on the BAS instead of paid upfront.
- Low-value goods (A$1,000 or less) bought from an overseas seller or marketplace are taxed at the point of sale for consumers (ATO low value imported goods). If you're buying stock for your business, give the supplier your ABN and confirm you're GST-registered so GST isn't charged. If it's charged anyway, ask for a refund.
- Duty and freight form part of the cost of your stock, not an expense on the day you pay them.
GST on what you sell
Sales to Australian customers are generally taxable, including the shipping fee you charge. Exports are generally GST-free if the goods leave Australia within the required time and you keep evidence. If you sell regularly into another country, that country's GST or VAT rules on low-value imports may apply to you as the seller.
Trading stock at 30 June
You must account for the value of stock on hand at year end, at cost, market selling value or replacement value, chosen item by item. Obsolete or damaged stock can be written down if you have evidence. Small businesses may use the simplified trading stock rules if the change in value is reasonably estimated at $5,000 or less.
GST registration and cash-basis reporting
If your GST turnover reaches $75,000 you must register. Our guide on when to register for GST explains how turnover is counted. Many online sellers start on cash-basis GST, which is simpler when payouts lag sales.
What's the right structure for an ecommerce business?
| Situation | Common structure | Why |
|---|---|---|
| Side business, modest profit | Sole trader | Low cost; losses may offset other income if the non-commercial loss rules are met |
| Growing store, profit retained for stock | Company | 25% tax rate for base rate entities, limited liability for supplier and product claims |
| Family business, profit to share | Company owned by a family trust | Flexibility in dividends, protection of the shares |
| Valuable brand, domains or IP | IP held separately and licensed to the trading company | Keeps the brand away from trading risk, with transfer pricing kept at market |
| Planning to sell | Clean company with its own records | Buyers pay more for clean, reconciled numbers |
If you're deciding now, read our guide to sole trader vs company vs trust.
How do we work with online retailers?
- Free strategy call to look at your platforms, stock and current reporting.
- Clean-up. We rebuild clearing accounts for each platform, reconcile historical payouts, and fix GST coding on imports and fees. If you're on MYOB or a spreadsheet, we can move you to Xero.
- Connect the apps. Marketplace connectors, inventory software, payment providers and bank feeds, mapped once and checked monthly.
- Daily bookkeeping with AI-suggested coding reviewed by a bookkeeper.
- BAS with a pre-lodgement check. Our BAS checking agent looks for GST errors such as credits claimed on overseas invoices with no GST, or exports coded as taxable. An accountant signs off.
- Monthly channel report and a rolling cash forecast. Our cash flow forecast agent builds the three-way model and your accountant reviews the assumptions with you.
Everything runs on Nagaris. The AI agents draft; qualified accountants review and sign off, and nothing goes to you or the ATO without a person approving it.
"It's been wonderful working with the BPAG team! They are true experts and have provided incredibly valuable business advisory and tax services, helping my business grow." Mitchell King, Google review
What does it cost?
Stores with up to about 100 transactions a month often fit Compliance Essentials from $149 per week + GST. Most growing sellers want monthly margin reporting and KPI analysis from Business Insights from $249 per week + GST. Larger brands planning stock, funding and expansion use Fractional CFO from $499 per week + GST. See the pricing page.
If you sell a few hundred orders a year through one platform, a connector app, cash-basis GST and an annual return may be enough. We'll tell you.
What should you send us?
- Xero access (or your current software)
- Admin or reports access for Shopify, Amazon Seller Central, eBay, Stripe, PayPal and any buy-now-pay-later provider
- Three months of payout or settlement reports
- Inventory system access and your latest stock valuation
- Recent import documents: supplier invoices, freight invoices and customs entries
- Your last four BAS and last year's tax return
Exports and photos from your phone are fine. No portal password to remember.
Frequently asked questions
Why doesn't my Shopify revenue match my bank deposits?
Because a payout is a net figure. It's gross sales less refunds, platform and payment fees, chargebacks and reserves, often covering several days of orders. If the payout is recorded as revenue, sales and fees are both understated and GST can be wrong. The fix is a clearing account that records gross sales and each deduction separately, then matches the net payout to the bank.
Do I charge GST on sales to overseas customers?
Goods you export are generally GST-free if you send them overseas within the required timeframe and keep evidence of export, such as shipping records. You may still have obligations in the customer's country, because many countries tax low-value imports at the point of sale. Check the rules for any market where you sell regularly.
Do I need to do a stocktake at 30 June?
You need to account for the value of trading stock at year end. Small businesses can use the simplified trading stock rules and skip the formal count where they reasonably estimate the change in stock value is $5,000 or less. Most online retailers with meaningful stock are well past that, so a count or a reliable inventory system figure is needed.
Can you work with inventory apps and A2X?
Yes. Connectors like A2X summarise marketplace settlements into clean journals, and inventory apps such as Cin7, Unleashed or similar track stock and cost of goods sold. We set them up so Xero holds the summary and the app holds the detail, then check that the two agree each month.
When should an online store move from sole trader to a company?
When profit is consistently well above what you need to live on, when you carry real liability (product claims, supplier contracts, stock finance), or when you want to keep profit in the business to fund stock. A company pays 25% tax as a base rate entity, but money taken out is taxed again, so it's worth modelling first.
Are payment platform fees GST-inclusive?
It depends on the provider. Australian-based platforms usually charge GST on their fees and give you a tax invoice. Some overseas providers don't charge GST to a business that has supplied its ABN. Only claim a GST credit where GST was actually charged and you hold the right invoice or statement.
Official sources
General information only, current as at 18 October 2026. It is not personal tax, legal or financial product advice and doesn't take your circumstances into account. Talk to us before you act. Where a recommendation needs a licensed financial adviser or a solicitor, we work alongside them.