How this usually works
A practical process for ecommerce starts with a short review: sales channels (Shopify, Amazon, eBay, Etsy, WooCommerce), payment processors (Stripe, PayPal, Afterpay), current accounting software (Xero or QuickBooks), inventory approach, GST status and any BAS or tax pressure.
Work then splits into three layers:
- Immediate triage: fix broken bank rules and GST codes, clean duplicate sales, reconcile marketplace payouts, and file any overdue BAS.
- Process design: connect channels with a suitable app (A2X, Dext Commerce or Synder), standardise your chart of accounts, map GST on AU and overseas sales, and configure inventory/COGS if you hold stock.
- Ongoing review: month-end close with channel reconciliations, BAS preparation, cash flow and margin reporting, and clear communication.
Australian context to keep in view
- GST registration is generally required at $75,000 turnover. Ensure your webstore charges GST correctly on AU sales and zero-rates eligible exports.
- Marketplaces may collect and remit GST on marketplace-supplied sales, but you must still report correctly on your BAS and claim eligible credits such as import GST on inventory.
- Inventory matters: recording landed cost (product, freight, insurance, duty) improves gross margin accuracy and tax outcomes.
- Payroll for growing online stores requires STP reporting, PAYG withholding and super compliance. See Payroll services if you are hiring.
- Use Australian-friendly systems: Xero or QuickBooks Online paired with connectors and, if needed, inventory tools such as DEAR/Cin7 Core or Unleashed.
What to compare before you commit
Scope
Confirm it truly covers ecommerce: channel integrations, payout reconciliation, GST/BAS, inventory and COGS setup, month-end close, and tax lodgements. Ask what is included versus once-off project work.
Software fit
Check depth with Xero/QuickBooks and your connector (A2X, Dext Commerce, Synder). If you hold stock, ask about inventory systems and landed cost. Request a simple data-flow diagram, not just software names.
Turnaround and communication
Agree on close dates (e.g., close by the 10th), BAS timelines, who approves changes, and how spikes (sales events, stock drops, refunds) are handled. Ask how handover works if your volume grows.
Commercial fit
Compare fixed-fee vs hourly, contract terms, and inclusions like connector subscriptions. Ensure you are getting proactive issue-spotting, not just reactive bookkeeping. If tax strategy matters, confirm a clear link to a tax accountant.
Best next steps
Write down the outcomes you want: accurate GST on every sale, clean marketplace and payment reconciliations, inventory and COGS working, on-time BAS, and clear margin and cash flow reporting.
Gather the essentials: access to Xero or QuickBooks, your store and marketplace admin, payment gateways, recent payout reports, and a list of SKUs or inventory approach. Note any deadlines or past ATO lodgements.
Shortlist providers against your channels and volume, not just a generic “small business accountant”. The right fit can explain your data flow in minutes and show examples of ecommerce month-end packs.
Frequently asked questions
What does a small business accountant for ecommerce actually do?
They connect stores and marketplaces to Xero or QuickBooks, map GST correctly, reconcile payouts and fees, configure inventory and COGS, prepare BAS and tax, and deliver timely reporting so online sales translate cleanly into your accounts.
How are Shopify, Amazon, eBay and PayPal payouts handled?
Use an integration tool to generate summary journals that split sales, GST, shipping, discounts, refunds and fees. Reconcile journals to clearing accounts and match them to bank deposits so each payout nets to zero without double counting.
Do I need to register for GST and how is marketplace GST treated?
You generally register at $75,000 GST turnover. Marketplaces may collect and remit GST on marketplace-supplied sales, but you remain responsible for BAS accuracy, correct codes on your own webstore, and claiming eligible import GST credits.
Which apps are best for ecommerce accounting?
Xero or QuickBooks Online plus A2X, Dext Commerce or Synder for channel summaries. If you hold stock, consider DEAR/Cin7 Core or Unleashed for deeper inventory and landed cost management.
Can you help with inventory, COGS and landed cost?
Yes. Proper setup capitalises landed cost into inventory, recognises COGS on sale, and uses stocktakes or perpetual adjustments to keep quantities accurate, improving margin reporting and tax outcomes.
What should I read next?
Use the links to bookkeeping services, BAS agent services and the help centre for deeper comparisons before you make contact.