How bookkeeping for ecommerce usually works
A solid process starts with a quick health check: business structure, sales channels, software stack, current reconciliations, inventory method, and any BAS or payroll deadlines.
Work typically falls into three layers:
- Immediate triage: fix unreconciled payouts, mis‑coded GST, broken bank rules, and stock imbalances.
- Process design: map channels via A2X or native connectors, tidy clearing accounts, define COGS method (perpetual or periodic), and set a monthly close checklist.
- Ongoing review: monthly reconciliations, COGS and stock checks, GST review and BAS prep, with a simple sales and margin summary by channel.
Need a quick assessment of your current setup in Xero or QuickBooks Online? We can review and outline a practical next step.
Australian context to keep in view
- GST on domestic sales and shipping, GST‑free exports, and LVIG rules affect coding and BAS.
- Marketplaces may collect/remit GST; you still need correct bookkeeping and evidence.
- Payment gateways and BNPL (Shopify Payments, Stripe, PayPal, Afterpay, Zip) require clearing accounts to net fees, refunds and chargebacks.
- Inventory and COGS: include landed costs, 3PL fees and returns; reconcile to stock reports.
- Payroll: if applicable, ensure STP, super and leave are kept current during peak sales cycles.
What to compare before you commit
Scope
Confirm the scope covers payout mapping (Shopify/Amazon/eBay/Etsy), GST review and BAS, inventory/COGS, clean‑up, monthly close, and simple channel reporting.
Software fit
Look for confidence with Xero or QuickBooks Online, A2X, Dext/Hubdoc, Shopify/Woo, Amazon Seller Central, and inventory tools like Cin7 Core or Unleashed.
Turnaround and communication
Agree on weekly/monthly rhythms, how peak periods are handled, and who reviews exceptions like chargebacks or stock variances.
Commercial fit
Compare fixed vs hourly, scope caps, and how advisory is handled beyond compliance (cash flow, margin trends, and channel mix insights).
What good ecommerce bookkeeping includes
- Channel‑level sales capture with accurate tax treatment and fee deductions.
- Gateway and marketplace reconciliation to the cent for every payout.
- Inventory and COGS reconciled to system reports and 3PL counts.
- Clear treatment for gift cards, deposits, pre‑orders, and customer credits.
- Refunds and returns posted to revenue and stock correctly.
- Monthly close with BAS‑ready GST checks and a simple performance summary.
If you also need payroll or tax support, use our specialist pages for payroll for ecommerce and tax and BAS for ecommerce.
Software and integrations we work with
We support Xero, QuickBooks Online and MYOB, with integrations across Shopify, Shopify POS, WooCommerce, Amazon, eBay and Etsy. For higher volume or multi‑warehouse needs we work with inventory systems such as Cin7 Core (DEAR), Cin7 and Unleashed.
- A2X for marketplace/channel posting and clearing accounts.
- Dext or Hubdoc to capture bills and receipts.
- Bank feed and rule reviews to prevent miscoding.
- Consistent GST codes for domestic and export sales.
Best next steps
Write down your top outcome: clean‑up, faster monthly close, confident BAS, clearer margins, or better inventory control. Shortlist providers who explain their mapping, close checklist and timelines plainly.
Use these related pages if you are still deciding: the Ecommerce Accountant hub, Bookkeeping Services, and our Help Centre. If you are ready to act, send a short brief now.
Frequently asked questions
Why does ecommerce bookkeeping need a specialist?
Ecommerce adds marketplace payouts, gateway fees, refunds and chargebacks, stock movements and GST differences across channels. A specialist maps these flows so the bank, clearing accounts, inventory and BAS match.
How are Shopify or Amazon payouts reconciled?
Record gross sales by channel, then net discounts, shipping, GST, marketplace fees and chargebacks to a clearing account. The net equals the bank payout. A2X can automate correct postings into Xero or QBO.
How do you track inventory and COGS properly?
Use a consistent method: perpetual via an inventory system (e.g., Cin7 Core/Unleashed) or periodic monthly COGS. Include landed costs, handle returns properly, and reconcile to system and 3PL reports.
What GST rules should ecommerce sellers watch?
Domestic GST on goods and shipping, GST‑free exports, LVIG, marketplace GST collection, gift card liabilities, and FX impacts for overseas gateways. Correct coding prevents BAS errors.
Which software stack works best?
Xero or QuickBooks Online with A2X for channel postings, Dext/Hubdoc for bills, and Cin7 Core or Unleashed if you need deeper inventory. The right mix depends on order volume, channels and warehousing.
How often should we close the books?
Monthly is standard for ecommerce. During peak periods, add weekly checks for payouts, GST coding and stock variances so issues don’t snowball.