Running an ecommerce business in Australia means getting GST compliance right from day one. From Shopify to Amazon, your GST obligations can get complicated fast, especially when selling across borders or using multiple payment platforms.

At JD Scott + Co, we specialise in ecommerce accounting and tax compliance for online sellers. This guide explains everything you need to know about how GST works for ecommerce businesses, plus practical steps to stay compliant and maximise your profits.

What Is GST and When Does It Apply to Ecommerce Businesses?

The Goods and Services Tax (GST) is a 10% tax on most goods and services sold in Australia. Read more about when you need to register for GST here.
If your ecommerce business has a turnover above $75,000 per year, you must register for GST with the Australian Taxation Office (ATO).

GST applies to:

  • Products sold through Shopify, WooCommerce, Amazon, or your own website

  • Digital products, online courses, and subscriptions

  • Marketplace transactions covered under “GST on low-value imported goods”

💡 Tip: Even if you’re under the $75,000 threshold, registering voluntarily can let you claim input tax credits on business expenses.

GST for International & Cross-Border Ecommerce Sales

If you sell to overseas customers or import goods into Australia, the GST treatment changes depending on where your buyers and suppliers are located.

Exports

  • Goods exported from Australia within 60 days of payment or invoice are generally GST-free.

  • You must keep documentary evidence showing that goods were exported within the required period.

Imports

  • GST may be payable at customs or through your freight forwarder.

  • Keep import declarations to claim GST credits later.

Foreign Sellers to Australia

  • Overseas sellers may need to register for GST under the low-value imported goods regime.

Keeping accurate and automated records is your best protection against ATO penalties.

How to Register for GST as an Ecommerce Business

You can register for GST online via the ATO Business Portal or through your accountant.

You’ll need:

  • ABN (Australian Business Number)

  • Business details and structure

  • Expected annual turnover

  • Bank details

Once registered, you must:

  1. Charge GST on taxable sales

  2. Issue tax invoices showing GST clearly

  3. Lodge Business Activity Statements (BAS) (usually quarterly)

  4. Remit GST to the ATO, minus credits on eligible purchases

 

GST Exports: Rules, Conditions & Best Practice

Selling internationally can boost your growth — and exports may be GST-free, provided you meet ATO rules.

When Are Exports GST-Free?

  • Goods exported within 60 days of invoice or payment

  • Services provided to overseas clients for use outside Australia

Relevant ATO provisions:

  • Section 38-185 (exports of goods)

  • Section 38-190 (supplies for consumption outside Australia)

  • GSTR 2002/6 and GSTR 2025/2

Key Conditions

  • Goods must leave Australia within 60 days after invoice/payment

  • You may apply for ATO extension if delays occur

  • For services, GST-free status depends on where the benefit is enjoyed

Evidence You Must Keep

  • Export documentation (bill of lading, airway bill)

  • Customs declarations or export clearances

  • Proof goods left Australia within 60 days

  • Invoices, contracts, and payment receipts

  • For services — evidence of overseas use

⚠️ Without proper proof, the ATO can disallow GST-free status and demand back payments.

Claiming GST Credits on Inputs

Even when sales are GST-free, you can still claim input tax credits for expenses like:

  • Materials, packaging, and shipping

  • Software and ecommerce tools

  • Marketing and advertising

Visit the ATO Law Database for detailed rulings and updates.

Common Ecommerce GST Mistakes

Avoid these common GST traps:

  • Not registering when turnover exceeds $75,000

  • Incorrect GST setup in Shopify or WooCommerce

  • Forgetting GST on freight

  • Not reconciling payment gateway fees

  • Claiming GST-free exports without documentation

✅ Pro Tip: Use an experienced ecommerce accountant to automate GST tracking and reconciliation.

GST and Ecommerce Platforms

Shopify: How to Set Up GST Correctly

Shopify doesn’t automatically manage GST for Australian sellers. You’ll need to configure your settings carefully.

Step-by-step:

  1. Enable GST Collection:
    Settings → Taxes and Duties → Regions → Australia → Enter ABN → Collect GST.

  2. Include GST in Prices:
    Display GST-inclusive pricing (e.g., $110 includes $10 GST).

  3. Charge Tax on Shipping:
    Ensure freight charges include GST.

  4. Update Invoice Templates:
    Add business name, ABN, address, and GST amounts.

  5. Integrate with Xero:
    Use Shopify + Xero to sync sales and GST automatically.

Avoid:
❌ Missing GST on shipping
❌ Mismatched tax settings
❌ Ignoring platform or payment fees

Amazon and WooCommerce

Amazon:
Amazon may collect and remit GST for some marketplace sales, but you must still ensure your BAS reports match ATO data, especially for direct website sales.

WooCommerce:
Use plugins like WooCommerce Tax or AvaTax. Set your default tax rate to 10% and confirm GST applies to both products and shipping.

Key Takeaways

AreaWhat You Need to Know
GST ThresholdRegister if turnover > $75,000/year
GST Rate10% on most goods and services
ExportsGST‑free if shipped within 60 days and you keep proof
BookkeepingIntegrate Shopify + Xero to stay ATO‑ready
Expert HelpUse an ecommerce accountant to avoid ATO issues

 

How JD Scott + Co Helps Ecommerce Businesses

We offer:

  • GST registration and BAS lodgement

  • Shopify, Amazon, and Xero integration

  • Cross-border tax advice

  • Automated bookkeeping

  • Strategic tax planning for ecommerce growth

Final Thoughts

Getting GST right is essential for every online seller in Australia. Whether you’re running a Shopify store or selling internationally, correct GST setup and documentation protect your business from ATO risk.

At JD Scott + Co, our Sydney ecommerce accountants help you stay compliant, save time, and grow confidently.

📞 Contact Us today to get started.