Top 7 E-Commerce Payment Gateways for Shopify & WooCommerce in Australia

Amelia had built her Melbourne candle and home-fragrance label from a kitchen bench to a six-figure Shopify store in under two years. The products were selling. The Instagram ads were converting. So why, she wondered one Tuesday night while reconciling her merchant statement, did her bank account never seem to match the revenue number in her dashboard?

The answer was sitting in plain sight across three different fee lines: a gateway percentage, an international card surcharge she didn’t know she was paying, and a Buy Now, Pay Later fee that had quietly eaten nearly six per cent of her margin on her best-selling candle set. Nobody had explained, when she first ticked the “enable payments” box during setup, that the checkbox she clicked would become one of the most consequential financial decisions in her business.

Amelia’s story is playing out in spare rooms and warehouses across the country right now, and it’s about to matter even more. From 1 October 2026, the Reserve Bank of Australia’s ban on card surcharging comes into effect for the major card networks, which means Australian merchants can no longer pass their processing costs on to customers at checkout. The fee your gateway charges will sit inside your product price, or it will sit inside your profit margin — there’s no third option. Choosing the right payment gateway has quietly gone from a technical setup task to a core pricing decision.

Why the Surcharge Ban Changes the Maths for Every Online Store

Until now, plenty of Australian merchants treated their gateway fee as a pass-through cost. A small surcharge line at checkout, a shrug, and the customer covered the difference. The RBA’s 2026 conclusions paper puts an end to that for card payments processed through the eftpos, Mastercard and Visa networks, with American Express following the same timeline voluntarily. Weekend surcharges and genuine service fees are unaffected, but the blanket “we charge 1.5% extra for card payments” approach is gone.

That means the difference between a gateway charging 1.5% and one charging 2.9% is no longer a line item you can shift onto someone else. It’s a direct hit to your gross margin, multiplied across every single transaction you process for the life of your business. On a store turning over $30,000 a month, that 1.4 percentage-point gap is worth roughly $5,000 a year — money that either stays in your business or quietly leaks out through a gateway you chose without comparing it properly.

The Platform Fork: How Shopify and WooCommerce Change Your Options

Before comparing individual providers, it’s worth understanding a structural difference between the two platforms named in this guide, because it changes which gateways are even realistically on the table for you.

Shopify is a closed ecosystem. If you use a third-party gateway instead of Shopify Payments, Shopify adds its own additional transaction fee — commonly around 2% depending on your plan — on top of whatever your chosen gateway charges. For most Shopify merchants, that makes Shopify Payments the default starting point, with other gateways typically bolted on as secondary options (PayPal as an express wallet, Afterpay or Zip as a BNPL layer) rather than full replacements.

The Line-Up: 7 Payment Options Worth Your Attention in 2026

Think of this less as a ranked leaderboard and more as a shortlist. Each of these plays a different role, and the right combination for a Sydney-based importer selling homewares will look different from the right combination for a Perth-based digital course creator. Figures below are current published rates at the time of writing and are quoted exclusive of GST unless stated; always confirm current pricing directly with the provider before committing.

1. Shopify Payments: The Path of Least Resistance for Shopify Stores

For any merchant building on Shopify, Shopify Payments is the gateway built into the platform from day one — no separate merchant account application, no extra integration fee. Online rates typically run from around 2.5% to 2.9% plus 30 cents per transaction depending on your plan tier, with a further currency conversion fee of roughly 2% if you’re settling in a currency other than AUD. Buy Now, Pay Later options like Shop Pay Installments are built straight into the checkout without needing a separate app.

The trade-off is flexibility: you’re locked into Shopify’s pricing structure, and the fee doesn’t come down meaningfully unless you move to a higher (and pricier) plan. For a store just starting out that wants payments working in ten minutes, it’s hard to beat. For a high-volume store watching every basis point, it’s usually the benchmark you’re trying to beat, not the final answer.

2. WooPayments: WooCommerce’s Native Answer, Built on Stripe’s Rails

WooPayments is WooCommerce’s own first-party gateway, running on Stripe’s global payment infrastructure. Domestic Australian cards are charged at roughly 1.75% plus 30 cents, with an additional 1.5% loaded on for international cards and a further 2% if the customer’s payment currency doesn’t match your payout currency. There’s no monthly fee, and because it’s native to WooCommerce, setup is close to Shopify Payments’ level of simplicity while sitting on genuinely competitive base rates.

It’s a strong first stop for most new WooCommerce stores — good documentation, wide payment method support, and pricing that beats Shopify Payments on domestic transactions. Where it can get expensive is a store with a lot of genuinely international customers, where the stacked international and conversion fees add up quickly.

3. eWAY: The Australian-Built Workhorse for Predictable Flat-Rate Fees

eWAY has been processing Australian online payments for over two decades, and its pricing reflects a very local, very deliberate philosophy: one flat rate regardless of card type. Domestic transactions run at around 1.5% plus 25 cents, whether the card is Visa, Mastercard or American Express — a detail that matters because plenty of gateways quietly charge more for Amex acceptance. International cards attract an additional surcharge of close to 2%. There’s no monthly fee and no lock-in contract, though a modest annual PCI compliance fee applies.

4. Airwallex: The Multi-Currency Ally for Importers Battling AUD Swings

Airwallex is built for a different problem entirely: businesses that hold, receive or pay in multiple currencies. Card processing runs from around 1.65% plus 30 cents on domestic cards up to roughly 3.4% plus 30 cents internationally, with a currency conversion markup of about 0.5% on major currencies — noticeably tighter than the 2-4% markups charged by some competitors. Plans start free or at roughly $29 a month, often waived above a minimum account balance.

For a business like a Sydney-based importer sourcing stock from overseas suppliers and worrying about AUD volatility eating into landed costs, Airwallex’s appeal isn’t just the checkout fee — it’s having a multi-currency account that can hold USD or CNY balances and reduce the number of times money gets converted back and forth. It’s less of a beginner’s plug-and-play option and more of a tool for a business that has outgrown simple single-currency processing.

5. Pin Payments: Lean, Local, and Refreshingly Simple

Pin Payments occupies a similar niche to eWAY but strips things back further: domestic cards at around 1.6% plus 30 cents, international cards at roughly 3.4% plus 30 cents, no monthly fees, and no setup costs. It’s a genuinely Australian-built product with a straightforward WooCommerce plugin, and its pricing page is refreshingly free of the tiered plans and add-on fees that make some competitors hard to compare at a glance.

It won’t out-feature Airwallex on multi-currency tools or out-scale Stripe on global reach, but for a small to mid-sized Australian store that wants low, predictable, all-inclusive pricing without reading a fee schedule twice, it’s consistently one of the simplest options on this list.

6. PayPal: The Trust Signal That Still Moves the Needle at Checkout

PayPal rarely wins on price — domestic transactions sit around 2.9% plus 30 cents, rising to roughly 3.9% plus a fixed fee internationally, with a currency conversion markup that can run 3-4% — but it wins on something else: recognition. A meaningful share of Australian shoppers, particularly those buying from a store for the first time, feel more comfortable entering their PayPal login than typing a card number into an unfamiliar checkout.

Most merchants on this list don’t run PayPal as their sole gateway; they run it alongside a lower-cost primary processor, treating it as a conversion tool for hesitant or first-time buyers rather than the workhorse handling every transaction. That’s usually the smarter way to use it.

7. Afterpay & Zip: The Conversion Booster That Comes at a Cost

Afterpay and Zip aren’t payment gateways in the traditional sense — they’re a Buy Now, Pay Later layer that typically sits on top of your core gateway. Merchant fees are steep by comparison: Afterpay generally charges 4-6% of the transaction plus 30 cents, and Zip sits in a similar 3.3-5.5% range plus a fixed fee, both considerably higher than the 1.5-2% most card processing costs. On a Shopify store, an additional platform transaction fee can stack on top of that again.

At a Glance: How the Fees Stack Up

Don’t Forget the Local Rails: PayTo, BPAY and the Australian Payment Stack

Your Decision Framework: Which Path Is Right for Your Store?

Rather than chasing the single “best” gateway, work through these questions in order. Each one narrows the field.

Question 1: Which platform is your store actually built on?

If you’re on Shopify, start with Shopify Payments as your baseline and only look elsewhere if a specific need — usually multi-currency exposure — justifies absorbing the platform’s third-party gateway fee. If you’re on WooCommerce, you have a genuinely open playing field; compare WooPayments, eWAY and Pin Payments on the merits before you commit.

Question 2: How international is your customer base and your supply chain?

A merchant like Lucas, running a purely domestic candle and homewares store, has little use for Airwallex’s multi-currency account — the simpler flat-rate pricing of eWAY or Pin Payments will usually serve him better. A merchant like Harper, importing furniture from Vietnam and shipping to customers across Australia and New Zealand, is dealing with currency exposure on both sides of the ledger and stands to gain far more from a multi-currency-aware provider.

Question 3: What’s your average order value and product category?

BNPL fees hurt far less on a $250 furniture order that converts because of the instalment option than on a $25 candle sale where the fixed fee alone eats a noticeable chunk of margin. If your average order value sits below roughly $60-$80, think carefully before adding Afterpay or Zip as a default option rather than an opt-in.

Question 4: Can you absorb the surcharge ban without repricing?

Run the numbers now, not in October. Take your current blended processing cost as a percentage of revenue and decide honestly whether it needs to be built into your retail pricing, or whether switching to a lower-cost gateway closes the gap without a price rise at all.

Question 5: How much do you value simplicity versus control?

If reading fee schedules isn’t how you want to spend your Sunday, Shopify Payments or Pin Payments’ flat, all-in pricing removes the guesswork. If you’re comfortable managing a slightly more complex setup for a meaningfully lower blended rate, eWAY or WooPayments reward that effort.

Compliance Doesn’t Disappear Just Because the Gateway Handles It

Your Gateway Handles Sales — Something Else Needs to Handle Your Supplier Payments

Once you’ve settled on a gateway, you’ve solved how money comes into your business. For a growing number of Australian e-commerce merchants — particularly importers like the one described above — the harder ongoing challenge is what happens on the other side: paying overseas suppliers in USD, CNY or EUR while the AUD moves against you week to week, and watching gateway currency conversion markups compound that exposure further.