Running an online store in Australia means choosing a payment gateway that keeps sales flowing, fees under control, and integrates cleanly with your bookkeeping. But with Stripe, PayPal, eWAY, Square, Afterpay, and other options, it can feel overwhelming.
This guide breaks down the best payment gateways in Australia in 2025, what makes them different, and how to pick the right one for your business.
What Is a Payment Gateway?
A payment gateway is the service that securely processes customer payments on your website or online store. It:
Connects your online store (Shopify, WooCommerce, Amazon, eBay, etc.) to your merchant account or bank.
Handles credit card, debit card, BNPL (Buy Now, Pay Later), and other online payment types.
Charges transaction fees (usually a % + fixed fee per transaction).
Choosing the wrong one can mean higher costs, more headaches with reconciliation, and unhappy customers.
Best Payment Gateways in Australia (2025)
Here’s a comparison of the most popular options for Australian small businesses:
Gateway | Best For | Key Features | Fees (Standard) | Integrations | |
|---|---|---|---|---|---|
Stripe | All-rounder for online stores | Easy setup, supports cards + wallets (Apple Pay, Google Pay) | 1.75% + 30c (domestic cards) | Shopify, WooCommerce, Xero (via A2X/Dext) | |
PayPal | Customer trust + quick checkout | Widely recognised, Pay in 4 (BNPL), instant setup | 2.6% + 30c (domestic) | Shopify, WooCommerce, eBay, Xero | |
eWAY (Australian-owned) | Local support + Australian merchants | Transparent pricing, direct phone support | From 1.5% + 25c | Shopify, WooCommerce, Xero | |
Square | Omnichannel (POS + online) | Free POS app, card readers for in-person + online sync | 1.9% per transaction | Shopify, WooCommerce, Xero | |
Afterpay | Buy Now Pay Later | Increases conversion, especially in fashion/retail | ~6% per transaction (higher than cards) | Shopify, WooCommerce | |
Shopify Payments | Shopify-only sellers | Built into Shopify, simple setup, fewer integrations needed | 1.75% + 30c | Shopify (native) |
Stripe vs PayPal vs eWAY: Quick Comparison
Stripe → Best balance of features, fees, and integrations. Great if you use Xero + multi-channel selling.
PayPal → Best for customer trust, but fees are higher. Some buyers only trust PayPal, so worth keeping.
eWAY → Australian-owned with strong local support. Competitive fees, good if you want a local partner.
Which Payment Gateway Has the Lowest Fees?
Stripe and Shopify Payments (1.75% + 30c) are usually cheapest for online stores.
PayPal (2.6% + 30c) is more expensive, but customers love it.
Afterpay has the highest fees (around 6%), but can boost sales.
Pro tip: Don’t just look at fees. Consider support, integration, and customer experience.
How Payment Gateways Affect Your Bookkeeping
This is where most e-commerce sellers get stuck:
Your bank sees a net payout (sales minus fees, refunds, chargebacks).
If you only record the net, your books are wrong.
You need to record gross sales, fees, GST, refunds — and reconcile them properly.
At Books Bean Kept, we:
Set up Xero with clearing accounts for each payment gateway.
Use integrations like A2X or Dext Commerce to automate the flow.
Ensure every fee, refund, and GST amount is tracked — so you always know your true profit.
FAQ
Does Stripe accept Amex in Australia? Yes — Stripe accepts American Express, but the fee is slightly higher (2.9% + 30c per transaction).
Which payment gateway is cheapest in Australia? Stripe and Shopify Payments usually have the lowest standard fees (1.75% + 30c).
Is eWAY better than Stripe? Stripe has more global integrations, but eWAY is Australian-owned with direct local support. It depends on whether you value global reach or local service.
Do I need multiple payment gateways? Often yes — many stores keep PayPal for trust + Stripe/Shopify Payments for lower fees.
Next Steps
Choosing the right payment gateway is only half the battle — making sure it integrates with Xero and your e-commerce platforms is where the real savings happen.
Download our free Payment Gateway Comparison Cheat Sheet (fees, features, integrations, all in one page).
Or, book a free discovery call and let us handle the setup and reconciliation for you.