The Best Payment Gateways for Australian Online Stores (2026)

Picking a payment gateway is one of the most important decisions for your online store. Pick wrong and you'll pay thousands more in fees over the years. Pick right and you can forget about it.

Here's an honest comparison of the 8 main options for Australian online stores in 2026.

Quick Comparison Table

Gateway	Fee (AU card)	Monthly Cost	Afterpay	Payout Speed
Stripe	1.75% + $0.30	$0	Yes	2 days
Square	2.2%	$0	Yes	1 day
PayPal	2.6% + $0.30	$0	No (has own)	1-3 days
Afterpay Direct	4-6% per transaction	$0	Native	1 day
Zip	Similar to Afterpay	$0	No	1-2 days
eWAY	1.75% + $0.25	$20	Via integration	2 days
NAB Transact	1.3%-1.8%	$40-100	No	1 day
Windcave (formerly DPS)	Negotiated	$30+	Via integration	1-2 days

The Detailed Breakdown

1. Stripe (Our Top Pick for Most Stores)

Fees: 1.75% + $0.30 AUD on Australian cards, 2.9% + $0.30 on international cards.

Monthly cost: $0.

Why we recommend it:

Best integration with modern platforms (Next.js, Shopify, WooCommerce, everything)

Native Apple Pay, Google Pay, Afterpay, Link

Dashboard is genuinely good

Fraud protection (Stripe Radar) is industry-leading

Australian support team

2-day payout to any Australian bank account

Downsides:

Holds payouts for 7 days if you're new (normal for most gateways)

Can close accounts for high-risk industries (CBD, certain supplements, etc.)

Best for: 95% of Australian online stores. Start here unless you have a specific reason not to.

2. Square (Good Alternative, Best for Physical + Online)

Fees: 2.2% for online card payments. 1.9% if using their in-person POS.

Monthly cost: $0.

Why choose it:

Unified POS + online

Simpler than Stripe (but also less powerful)

Same-day deposit available

Good for retail businesses adding online

Downsides:

Higher fees than Stripe (for pure online)

Less third-party integration

Customer support can be slow

Best for: Physical stores adding an online presence. Not ideal for pure e-commerce.

3. PayPal (Avoid for Primary, OK as Secondary)

Fees: 2.6% + $0.30 AUD (standard), up to 3.5% for international cards.

Monthly cost: $0.

Why some use it:

Brand recognition (older customers trust it)

International sales

Buyer-initiated payments

Why we don't recommend it as primary:

50%+ higher fees than Stripe

Seller-unfriendly dispute resolution

Clunky checkout redirect (increases cart abandonment 20-30%)

Has "Pay in 4" but not Afterpay (Aussies prefer Afterpay)

Older, slower API

Best for: Offering as a secondary option. Don't make it primary.

4. Afterpay Direct

Fees: 4-6% per transaction (plus a small fixed fee).

Why use it:

30% of Australian online shoppers use Afterpay

Higher average order value (40%+ typically)

Marketing boost from Afterpay listing your store

Why not use it standalone:

Much higher fees than regular card processing

Only for qualifying transactions

Most customers still want card option

Best practice: Offer Afterpay THROUGH Stripe (cheaper than going direct). You get Afterpay at standard Stripe card fees.

5. Zip (Competitor to Afterpay)

Similar to Afterpay. Smaller market share but worth offering if your customer base skews older (30-50).

Best practice: Include via integration, not standalone.

6. eWAY (Australian-Owned Alternative)

Fees: 1.75% + $0.25 (similar to Stripe)

Monthly cost: $20

Why some choose it:

Australian-owned (helpful for some B2B government contracts)

Strong fraud protection

Good for subscription businesses

Downsides:

Monthly fee (Stripe doesn't charge one)

Less modern API than Stripe

Smaller ecosystem of integrations

Best for: Businesses requiring Australian-owned providers. Most don't need this.

7. NAB Transact (Big Bank Option)

Fees: 1.3%-1.8% (negotiated based on volume)

Monthly cost: $40-100/month

Why some choose it:

Potentially lower fees at high volume ($1M+/year)

Existing NAB relationship

Enterprise support

Why most shouldn't:

Monthly fees

Complex integration

Overkill for sub-$500K/year businesses

Cancellation fees

Best for: Established businesses doing $1M+/year with volume discounts.

8. Windcave (Formerly Payment Express/DPS)

Fees: Negotiated (usually competitive at volume)

Monthly cost: $30+

Best for: High-volume enterprise businesses. Overkill for small online stores.

Decision Framework

For 95% of Australian online stores, use Stripe.

Unless you fit one of these edge cases:

Use PayPal as secondary if:

You sell internationally

Your customer base skews 55+

Use Square if:

You have physical + online presence

You want unified POS

Use eWAY if:

B2B government contracts require Australian-owned

You need specific compliance requirements

Use NAB Transact if:

You're doing $1M+/year

You want to negotiate custom rates

The Fees Really Add Up

Here's what different choices cost at different volumes:

$50,000/year in revenue

Gateway	Annual Fees	Savings vs PayPal
Stripe	$1,025	$475
PayPal	$1,500	baseline
Square	$1,250	$250

$200,000/year in revenue

Gateway	Annual Fees	Savings vs PayPal
Stripe	$4,100	$1,900
PayPal	$6,000	baseline
Square	$5,000	$1,000

$1,000,000/year in revenue

Gateway	Annual Fees	Savings vs PayPal
Stripe	$20,500	$9,500
PayPal	$30,000	baseline
Square	$25,000	$5,000

At $1M/year, switching from PayPal to Stripe saves nearly $10,000. Enough for a holiday or a junior staff member.

Integration Effort

Easiest (Minutes)

Stripe Checkout — single line of JavaScript, hosted checkout page

PayPal Button — copy-paste

Square — WooCommerce/Shopify plugins

Medium (Hours)

Stripe Elements — custom checkout embedded in your site

eWAY — good docs, standard integration

Complex (Days)

NAB Transact — older APIs, custom work often required

Windcave — enterprise-level complexity

For a small business, Stripe Checkout is the right starting point. You can migrate to Stripe Elements later if you want fully custom checkout.

The Hidden Costs Nobody Mentions

Chargebacks

When a customer disputes a charge:

Stripe: $15 AUD fee (won or lost)

PayPal: $20 AUD fee + often ruled against seller

Square: $15 AUD fee

International Card Fees

Customers paying with foreign cards cost more:

Stripe: 2.9% + $0.30 (vs 1.75% for AU cards)

PayPal: Up to 4.5%

Square: 2.9%

If 20% of your customers are international, this adds up.

Currency Conversion

If you sell in USD but your bank is in AUD:

Stripe: ~2% conversion spread

PayPal: 3-4% conversion spread

Worth considering if you target US/UK customers.

Our Recommendation

Start with Stripe. Enable Afterpay, Apple Pay, Google Pay, Link. Offer PayPal as a secondary option only if customers specifically request it.

When you hit $500K/year: Review your setup. You might negotiate custom Stripe rates, or add eWAY for diversification.

When you hit $1M+/year: Consider NAB Transact alongside Stripe for volume discounts.

Don't overthink this decision. For a new store, Stripe + Afterpay is 95% of the answer.

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