E-Commerce Accounting Mistakes That Cost You Money

🛒 What Every Australian Online Business Owner Must Fix in 2026

If you run an online business in Australia, your accounting system is either helping you scale — or silently draining your profit.

At 42 Advisory (Chadstone, Melbourne), we see the same costly mistakes repeated across e-commerce brands.
Here are the ones that hurt the most — and how to fix them.

❌ Mistake #1 — Treating E-Commerce Like Regular Business Bookkeeping

One of the most expensive errors e-commerce founders make is assuming that online businesses can be run on the same accounting model as a traditional service or retail company.

E-commerce accounting is different.
It involves:

• Payment gateways (Stripe, PayPal, Afterpay, Zip, Klarna, Shopify Payments)

• Chargebacks 😩,  refunds, and disputes

• Platform and transaction fees

• Inventory across multiple locations and countries

• Cross-border GST and FX movements, multicurrency wallets

• Marketplace settlements that never match your bank deposits

When these elements are processed using old-school bookkeeping rules, your numbers stop telling the truth.

We frequently see businesses showing:

• inflated revenue,

• understated costs,

• incorrect GST,

• and “profitable” months that are actually cash-flow negative.

That’s not bookkeeping — that’s financial blindness.

Fix:
Implement a purpose-built e-commerce accounting system and processes. 

❌ Mistake #2 — Underestimating Chargebacks, Fraud & Payment Risk

Most e-commerce founders don’t realise this until it hurts:

Visa, Mastercard and Amex protect the cardholder — not the merchant.
In almost every online dispute, the merchant carries the risk.

This means your business is exposed to:

• Online fraudsters and friendly fraud

• Stolen card transactions

• Disputed deliveries

• Damaged goods returned

• Parcels lost in shipment

• Delayed settlements from merchant facility providers

And while platforms like Stripe, PayPal, Afterpay and Shopify Payments make selling easy, they do not absorb the financial damage.
They simply deduct it from your next payout or charge back you bank account.

How This Quietly Destroys Profit

In poorly structured e-commerce bookkeeping, we regularly find:

• Chargebacks recorded as “expenses” instead of revenue reversals

• Refunds are not linked to the original sale

• Payment processor fees are never fully reconciled

• GST not adjusted correctly

• Delayed payouts are not matched to the underlying transactions

The result is a dangerous illusion:

• Revenue is overstated

• GST is incorrect

• Margins are distorted

• Cash flow looks healthier than it really is

This is one of the fastest ways e-commerce businesses lose money without noticing.

Why E-Commerce Businesses Are Especially Vulnerable

Unlike in-store transactions, online merchants carry full delivery risk.
If the customer claims non-delivery, fraud, or damage, the platform almost always rules in their favour — and the money is clawed back from you.

You lose:

• the product,

• the shipping cost,

• the sale,

• the platform fee,

• and often the original transaction fee.

Without specialist e-commerce accounting, these losses are rarely measured accurately.

How 42 Advisory Protects Your Business

At 42 Advisory, we design chargeback-safe accounting systems that:

• Reconcile every sale, refund, fee, dispute and payout

• Reverse revenue correctly when disputes occur

• Adjust GST automatically

• Track true net margins

• Expose real cash flow (not platform illusions)

We also work with clients to strengthen transaction verification, fraud filters, and dispute documentation — reducing losses before they happen.

Because protecting profit starts with protecting your data.

❌ Mistake #3 — Getting GST Wrong on Imports & Dropshipping

Since 1 July 2018, GST applies to low-value imported goods sold to Australian consumers — including many dropshipping models.

We frequently uncover:

• missing GST on imports,

• incorrect supplier treatment,

• unreported customs obligations.

These errors trigger ATO penalties and cash-flow shocks.

❌ Mistake #4 — Selling Overseas Without Understanding Export GST

Most exports are GST-free, but that does not mean tax-free.

Poor FX handling and export classification errors cause:

• overstated GST,

• inaccurate profit reporting,

• bad decisions.

❌ Mistake #5 — Multi-Warehouse Inventory Confusion

With Amazon FBA, 3PLs, overseas suppliers, and multiple warehouses, inventory errors explode:

• COGS becomes unreliable,

• margins disappear,

• forecasts collapse.

If your inventory is wrong, your entire business model is wrong.

❌ Mistake #6 — No Advisory Layer

Most accountants stop at compliance.

Without forecasting, cash-flow modelling, and advisory support, e-commerce founders operate blind — even when sales are growing.

🧠 How 42 Advisory Solves This

We specialise in ecommerce accounting for Melbourne online businesses with fixed-fee packages that combine:

• Shopify & Xero integration

• Chargeback & gateway reconciliation

• Inventory & COGS accuracy

• GST, BAS & tax optimisation

• Investment-grade 3-way forecasting

• Strategic business advisory

We go beyond bookkeeping — we become your ecommerce accountant, tax specialist, and business advisor in one system.

👉 Learn how 42 Advisory can help E-Commerce