Why use an ecommerce accountant instead of a generalist?

Ecommerce businesses face multi-channel sales, settlement delays, foreign currency, inventory costing, marketplace fees and GST on cross-border sales. An ecommerce accountant understands these patterns, the software stack and the compliance calendar, so issues are solved faster and reported correctly.

How should Shopify, Amazon or eBay sales be reconciled?

Use a connector like A2X or Link My Books to summarise payouts by settlement period. Post gross sales, refunds, discounts, GST, shipping income and marketplace/merchant fees to the right accounts, then match them to bank deposits in Xero, MYOB or QuickBooks.

Do I charge GST on overseas orders?

Exports to customers overseas are generally GST-free if the goods are exported from Australia within the required timeframe. Low value goods rules can apply when you sell into Australia from overseas via an electronic distribution platform. An ecommerce accountant can map GST codes by channel and destination.

What inventory method works best for ecommerce?

For growing stores, perpetual inventory with landed cost (including freight, duties and handling) gives cleaner margins. Tools like Cin7 Core, Unleashed or inbuilt Shopify inventory can work, depending on complexity. Your accountant should align COGS recognition with actual stock movement.

What should I check before choosing an ecommerce accountant?

Check platform experience (Shopify, Amazon, eBay, WooCommerce), connector depth (A2X, Link My Books), inventory know-how, GST/BAS expertise, reporting cadence, turnaround time, and whether you need bookkeeping, payroll and tax under one roof.

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How ecommerce accounting usually works

A strong ecommerce accountant starts with a short discovery on structure, channels, software, inventory process, current pain points and looming deadlines. From there, the work typically falls into three stages:

1) Immediate triage. Fix settlement posting, clean bank rules, correct GST codes, reconcile stock and address urgent BAS or payroll issues.

2) Process design. Implement or refine connectors (A2X or Link My Books), set a clear chart of accounts, map tax codes by channel and country, and decide inventory method (periodic vs perpetual with landed costs).

3) Ongoing review. Monthly reconciliations, BAS lodgements, payroll/STP and a simple trading P&L that shows revenue, COGS, fees and ad spend by channel.

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Core tasks your ecommerce accountant should handle

Settlement reconciliation: Map gross sales, discounts, refunds, GST/VAT, shipping and marketplace/merchant fees, then match to bank deposits.
Inventory and COGS: Track stock on hand, landed costs (freight, duty, handling), kits/bundles and returned items to keep margins accurate.
GST and BAS: Apply correct GST codes by destination and platform; prepare and lodge BAS on time (monthly or quarterly).
Payroll for operations: STP, super and award considerations for in-house fulfilment, customer service and warehousing teams.
Reporting by channel: Separate performance for Shopify vs Amazon vs eBay; track contribution margin after ad spend.
Cash flow: Align purchase orders, stock cycles and ad spend with incoming settlements and tax obligations.

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Australian context to keep in view

GST on exports: Many exports are GST-free, but rules differ by timing and destination. Ensure channels apply correct codes.
Low value imported goods: When selling into Australia via electronic distribution platforms, GST may be collected by the platform.
BAS, PAYG and STP: Keep monthly or quarterly BAS cycles aligned with settlement rhythms; run STP and super on time.
State payroll tax and FBT: As headcount grows, watch state thresholds and benefits that may trigger FBT or payroll tax.

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Recommended ecommerce software stack

Accounting

Xero, MYOB Business or QuickBooks Online with a clean ecommerce chart of accounts and bank feeds.

Connectors

A2X or Link My Books for Shopify, Amazon and eBay settlements; Dext or Hubdoc for bills and receipts.

Inventory

Cin7 Core, Unleashed or inbuilt Shopify inventory for perpetual tracking and landed costing as complexity grows.

Analytics

Channel P&L and cohort metrics: gross margin after COGS and fees, contribution margin after ads, stock turns and cash conversion cycle.

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What to compare before you commit

Scope

Confirm ecommerce bookkeeping, BAS, payroll and tax are included. Ask about inventory support and month-end close.

Software fit

Look for hands-on experience with your platforms and connectors, not just brand names.

Turnaround and communication

Clarify meeting rhythm, response times and how urgent settlement or BAS issues are escalated.

Commercial fit

Compare pricing (fixed, tiered or hourly), reporting depth and whether you need compliance only or advisory support as well.

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Key metrics for ecommerce owners

Gross margin after COGS and fees (include merchant and marketplace fees).
Contribution margin after ad spend by channel or campaign.
Inventory turnover and weeks of cover to balance stockouts and cash tied up.
Refund rate and returns impact on margin and inventory.
Cash conversion cycle from supplier payment to settlement receipt.

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Best next steps

Write down your top outcomes: tidy settlements, accurate stock and COGS, clean BAS, payroll confidence, better channel reporting or a lightweight finance plan for growth.

Shortlist providers who explain exactly how they’ll treat settlements, GST and inventory in your context. Ask for an example channel P&L and a 90‑day plan.

Use the related pages below to dive into ecommerce bookkeeping, payroll and tax, or go straight to the form to request help.

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Frequently asked questions

Why does ecommerce accounting need a specialist lens?

Ecommerce mixes multiple sales channels, settlement delays, marketplace and merchant fees, foreign currency, inventory and complex GST. An ecommerce accountant understands these moving parts and sets up workflows that keep BAS, payroll and reporting accurate.

Is industry experience more important than software knowledge?

Both matter. Industry context drives the right chart of accounts, tax codes and inventory method. Software depth ensures fast, accurate reconciliations with tools like A2X, Link My Books, Xero, MYOB and QuickBooks.

Should my ecommerce accountant also handle bookkeeping or payroll?

Many sellers prefer one coordinated team. A lead ecommerce accountant can steer bookkeeping, BAS and payroll so settlements, stock and wages align with cash flow and compliance.

How do I compare providers quickly?

Ask for their approach to settlements, GST mapping by channel, inventory/COGS, month-end timelines and a sample channel P&L. Check registrations and relevant platform experience.

Can you fix historic periods and overdue BAS?

Yes. Triage typically includes back-reconciling settlements, correcting GST codes, posting inventory adjustments and lodging overdue BAS with a clear plan to prevent repeats.