6 best payment gateways for Shopify Malaysia (2026)

Key Takeaways:

• Shopify Payments is not available in Malaysia, so you’ll need to choose a third-party payment gateway to accept payments.

• Malaysian shoppers prefer local methods like FPX, DuitNow, and e-wallets, so your gateway needs to support them or you risk losing sales at checkout.

• Airwallex integrates directly with Shopify as a payment gateway, letting you accept payments from customers in Malaysia and worldwide — with like-for-like currency settlement and no hidden foreign exchange fees.

Choosing the right payment gateway for your Shopify store in Malaysia is one of the most important decisions you'll make as a merchant.

Unlike store owners in some other countries, Malaysian merchants cannot use Shopify Payments, which means you need to use a third-party gateway.

This article focuses specifically on payment gateways: what to look for, which providers are available, how they compare on fees and local payment method coverage, and how to connect one to your Shopify settings.

For a full walkthrough of setting up a Shopify store in Malaysia, including plan costs, SST configuration, and logistics options, see our complete Shopify Malaysia guide.

What to look for in a Shopify payment gateway in Malaysia

Choosing a payment gateway isn't just about which one accepts the most card types. For Malaysian businesses on Shopify, a few specific factors make a bigger difference to your bottom line.

Transaction fees

Shopify charges a transaction fee whenever you use a third-party payment provider (i.e., anything other than Shopify Payments, which isn't available in Malaysia). That fee is:

• 2% on the Basic plan

• 1% on the Grow plan

• 0.6% on the Advanced plan

• 0.2% on Shopify Plus

This is on top of whatever processing fee your gateway charges. So if your gateway charges 2.5% per transaction and you're on the Basic plan, your real cost per sale is 4.5%. The gateway you choose — and the plan you're on — directly affects your margins.

Local payment method support

Malaysian shoppers expect to pay with what's familiar. FPX (the national online banking network) and e-wallets like Touch 'n Go, GrabPay, and Boost are widely used, especially for everyday purchases. If your gateway doesn't support these, you'll lose customers at checkout.

Currency and payout options

Check whether the gateway can settle in MYR and how quickly it pays out. Some gateways hold funds for several days; others offer next-day or same-day payouts. If you're also selling internationally, look for one that handles multi-currency transactions cleanly.

Shopify compatibility

Not all payment gateways have a native Shopify integration. The best ones offer a certified plugin or are listed directly in Shopify's payment providers settings, which means simpler setup and fewer technical issues down the line.

Customer support and local presence

Payment issues happen, and when they do, you need support that understands the Malaysian market. Gateways with local teams or Malaysia-based support lines tend to resolve issues faster than those routing everything through international centres.

Compliance and security

Look for PCI DSS compliance as a baseline. For gateways processing Malaysian transactions, Bank Negara Malaysia (BNM) also sets regulatory requirements — particularly for larger payment service providers. A reputable gateway will be transparent about its compliance standing.

How Malaysian shoppers prefer to pay

If you sell to Malaysian customers, your checkout needs to reflect how they actually pay.

Card payments are common, but a large share of Malaysian shoppers prefer local banking and wallet options — especially for everyday purchases.

1. FPX (Financial Process Exchange)

Financial Process Exchange, or FPX, is Malaysia's national online banking network, operated by PayNet. It lets customers pay directly from their bank account via a secure redirect to their own online banking portal.

FPX is widely trusted across Malaysia and is the default payment method for many eCommerce transactions. Most Malaysian Shopify merchants treat FPX support as non-negotiable.

2. DuitNow

DuitNow is the national real-time payment rail in Malaysia, also operated by PayNet. It includes DuitNow Transfer (for peer-to-peer and business transfers) and DuitNow QR (a standardised QR code that works across banks and e-wallets).

DuitNow QR is increasingly the preferred payment method at physical checkouts and is growing in online use too.

3. E-wallets

Malaysia has a well-developed e-wallet ecosystem. The major wallets accepted at most Shopify gateways include:

• GrabPay — widely used, linked to the Grab super-app

• Touch 'n Go eWallet — one of Malaysia's most popular, also used for toll and transit payments

• Boost — popular with younger demographics

• ShopeePay — strong reach among Shopee users

Customers paying by e-wallet expect a fast, seamless experience. If your checkout doesn't offer these options, a meaningful portion of shoppers will drop off.

4. Buy Now, Pay Later (BNPL)

BNPL adoption in Malaysia is growing fast. Key providers include Atome, Grab PayLater, and SPayLater (Shopee Pay Later).

For merchants, supporting BNPL can increase average order values — but check whether your gateway supports it and what fees apply before activating it.

The best payment gateways for Shopify in Malaysia

No single gateway is right for every Malaysian Shopify merchant. The best choice depends on your customer mix, sales volume, and whether you sell locally, internationally, or both.

Here’s a quick overview, before we go into the individual payment gateways:

The information in this table has been reviewed to be accurate as of 27 April 2026.

1. Airwallex

Airwallex is the strongest option for Malaysian Shopify merchants who sell — or plan to sell — beyond Malaysia. It connects to your Shopify store via its native plugin and supports both local Malaysian payment methods (FPX and DuitNow) and 160+ international payment methods, so you don't need a separate gateway for local and cross-border transactions.

Unlike most gateways, Airwallex settles like-for-like in 20+ currencies. If a customer pays in US dollars, you receive US dollars, with no forced conversion to ringgit at point of settlement.

The information in this table has been reviewed to be accurate as of 27 April 2026.

2. HitPay

HitPay is a Singapore-based payment platform with strong Malaysia coverage. It was built with small and medium businesses in mind and offers a simple, pay-per-transaction model with no setup or monthly fees.²

Its local payment method coverage is one of its strongest points: FPX, DuitNow QR, all major e-wallets, and BNPL options (Atome, Grab PayLater, SPayLater) are available under one integration. HitPay also integrates with Shopify directly and offers next-day payouts in most cases, which is useful for cash flow.

The information in this table has been reviewed to be accurate as of 27 April 2026.

3. Billplz

Billplz is a homegrown Malaysian payment platform focused on simplicity and local banking integration. It is particularly well-known for FPX, charging between RM0.75 to RM1.25 per FPX transaction³. Billplz also applies an additional 0.3% surcharge on transactions processed through Shopify specifically.

It has been used widely by Malaysian small businesses, NGOs, and schools. Billplz is a solid choice for merchants whose primary customer base pays by FPX and whose checkout volume is high enough to benefit from flat-fee pricing. Note that Billplz does not support DuitNow QR.

The information in this table has been reviewed to be accurate as of 27 April 2026.

4. ADAPTIS (formerly iPay88)

ADAPTIS — which replaced iPay88 following NTT DATA's acquisition — is Malaysia's most established payment gateway. It has the longest track record of any local provider, with deep relationships across Malaysian banks and a broad coverage of local payment methods including FPX, DuitNow, and most major e-wallets.

Enterprise merchants and larger retailers often choose ADAPTIS for its reliability and bank-grade infrastructure. Setup requires an application and merchant approval process, which can take one to four weeks.

The information in this table has been reviewed to be accurate as of 27 April 2026.

5. Stripe

Stripe is one of the world's most widely used payment platforms and is available in Malaysia. Its standard rate for card payments and FPX transactions is 3% + RM1.00 per successful transaction,¹ with no setup or monthly fees.

Stripe activates instantly — there’s no merchant approval period — which makes it the fastest gateway to get running. The trade-off is that it does not support DuitNow QR natively, and e-wallet coverage for Malaysian methods (GrabPay, Touch 'n Go) may be more limited compared to local-first alternatives.

The information in this table has been reviewed to be accurate as of 27 April 2026.

6. PayPal

PayPal is recognised worldwide and is useful for Malaysian merchants selling to international customers. Its standard rate for receiving domestic transactions in Malaysia is 3.90% + RM2.00 per transaction, plus a currency conversion fee of 2.5% above the base exchange rate if currency conversion is involved.⁴

It does not support FPX or DuitNow, which limits its usefulness as a primary gateway for a Malaysian-first customer base — most local shoppers prefer to pay via online banking or e-wallets. PayPal works best as a secondary gateway for merchants who sell to international buyers and need a globally recognised checkout option.

The information in this table has been reviewed to be accurate as of 27 April 2026.

How to set up a payment gateway on Shopify in Malaysia

Once you've chosen your gateway, connecting it to your Shopify store is straightforward. Here's how to do it:

Step 1: Go to your payment settings

Log in to your Shopify admin. From the left-hand menu, go to Settings → Payments.

Step 2: Select a payment provider

Under the Payment providers section, click Choose a provider. You'll see a list of supported third-party gateways. Search for your chosen provider — HitPay, Billplz, Stripe, PayPal, and ADAPTIS are all listed.

Step 3: Create or connect your gateway account

If you don't already have an account with your chosen gateway, you'll be redirected to their website to sign up. For local Malaysian gateways like HitPay and Billplz, you'll need to provide your business details and complete identity verification before your account is approved.

Step 4: Complete merchant approval (if required)

Activation timelines differ based on what gateway you’re using:

• Stripe and PayPal activate immediately.

• ADAPTIS has a formal merchant application process that can take one to four weeks.

• HitPay and Billplz are generally faster than ADAPTIS but still require document submission and approval.

Apply early so you're not holding up your store launch.

Step 5: Enter your gateway credentials

Once your gateway account is approved and active, return to Settings → Payments in your Shopify admin.

Enter the API keys or credentials provided by your gateway. These are usually found in your gateway's dashboard under "Developer settings" or "Integration".

Step 6: Configure payment methods

Within your gateway's settings, select which payment methods to activate: FPX, DuitNow, specific e-wallets, cards, and so on. Only activate methods your gateway has approved for your account.

Step 7: Set your currency

Make sure your Shopify store is set to accept Malaysian Ringgit (MYR) as your primary currency. Go to Settings → Store details → Store currency. If you sell internationally, you can add additional currencies depending on your plan.

Step 8: Test before going live

Before launching, place a test order using your gateway's sandbox or test mode. Confirm that:

• The payment page loads correctly

• Local payment methods appear at checkout

• The order is recorded in your Shopify admin after a successful test payment

Most gateways provide test card numbers or a sandbox environment for this purpose.

Step 9: Go live

Once testing passes, switch your gateway to live mode and you're ready to accept payments.

Why Malaysian businesses choose Airwallex for Shopify

Local gateways like HitPay and Billplz do a solid job if you're selling primarily to Malaysian customers who pay by FPX or e-wallet. For a domestic-first store, they're a practical, cost-effective choice.

But most businesses don't stay domestic-only. As your Shopify store grows, you'll likely start attracting customers from Singapore, Australia, the US, or elsewhere — and that's where local gateways start to show their limits.

That's where Airwallex comes in. It connects to your Shopify store as a payment gateway and gives you the infrastructure to handle both local and international payments in one place.

Here’s what you can do with Airwallex:

Accept 160+ local payment methods

Airwallex's Shopify Payment Plugin lets you accept payments from customers in Malaysia and internationally through a single integration.

You get access to 160+ local payment methods across markets, so international customers can pay the way they're used to, not just the way your local gateway allows.

Collect in the currency your customers pay in

Most payment gateways convert foreign currency into ringgit at the point of settlement. That means every international sale triggers an FX conversion — often at a rate that includes a markup — before the money even reaches your account.

Airwallex settles like-for-like in 20+ currencies. If a customer pays in US dollars, you receive US dollars. If they pay in Singapore dollars, you hold Singapore dollars. You decide when and whether to convert, which means you're not losing a percentage of every international sale to an automatic conversion you didn't ask for.

Transparent, competitive pricing

Airwallex charges 1.90% + RM0.50 for domestic cards and wallets, and from 1.4% + RM0.50 for local payment methods, with no setup fees, no monthly fees, and no hidden FX markups at the gateway layer. You can see exactly what each transaction costs before you commit.

When you factor in Shopify's third-party transaction fee on top of your gateway fee, keeping your gateway rate competitive matters. Lower gateway rates mean more of each sale stays with you.

Regulated in Malaysia

Airwallex is licensed in Malaysia by Bank Negara Malaysia for merchant acquiring. For merchants evaluating an international provider, that's a meaningful trust signal — it means Airwallex operates under the same regulatory framework as locally-established gateways and is held to the same compliance standards.

Managing your full payment operation

As your store scales, your payment needs go beyond checkout. You may need to hold foreign currency revenue without converting it immediately, pay overseas suppliers in their local currency, or manage ad spend across platforms like Meta and Google in US dollars.

Airwallex's broader platform — including Global Accounts, FX transfers, and corporate cards — is built for exactly that.

Frequently asked questions (FAQs)

What is the best payment gateway for Shopify in Malaysia?

There's no single answer — the right gateway depends on your customer mix. If most of your customers are Malaysian, you need a gateway that supports FPX and DuitNow, such as HitPay, Billplz, or ADAPTIS. If you sell internationally, consider adding a secondary gateway like Stripe for card payments, or using Airwallex as a single integration that covers both local and international transactions.

Does Shopify charge transaction fees in Malaysia?

Yes. Because Shopify Payments is not available in Malaysia, Shopify charges a third-party transaction fee on every sale: 2% on the Basic plan, 1% on the Grow plan, 0.6% on the Advanced plan, and 0.2% on Shopify Plus. This is separate from your gateway's own processing fee, so your real cost per transaction is the two fees combined.

How do I set up FPX on Shopify in Malaysia?

Shopify does not support FPX natively. To accept FPX payments, you need to connect a third-party gateway that supports it — HitPay, Billplz, and ADAPTIS all do. Once your gateway account is approved, you connect it to your Shopify store via Settings → Payments, then activate FPX within your gateway's settings dashboard.

Can I use two payment gateways on Shopify at the same time?

Yes. Shopify allows one primary payment provider and one secondary provider running simultaneously. The most common setup for Malaysian merchants is a local gateway (for FPX, DuitNow, and e-wallets) as the primary, with Stripe or PayPal as secondary for international card payments. Both can be active at checkout without requiring any custom development.

How long does payment gateway approval take in Malaysia?

It depends on the provider. Stripe and PayPal activate almost instantly. HitPay and Billplz are generally faster than traditional gateways but still require document submission and account verification. ADAPTIS has the longest approval timeline — typically one to four weeks — due to its formal merchant application process. If you're launching a new store, apply early.

Which Shopify payment gateway has the lowest fees in Malaysia?

Billplz has the lowest flat rate for FPX transactions at RM0.75 to RM1.25 per transaction,³ which makes it very cost-effective for stores with high FPX volume. For card payments, rates vary across providers — always calculate the combined cost of your gateway fee plus Shopify's third-party transaction fee to get your true per-sale cost.

Sources:

1. stripe.com/en-my/pricing

2. hitpayapp.com/my/pricing

3. billplz.com

4. paypal.com/my 

This publication does not constitute legal, tax, or professional advice from Airwallex nor substitute seeking such advice, and makes no express or implied representations / warranties / guarantees regarding content accuracy, completeness, or currency. If you would like to request an update, feel free to contact us at [[email protected]]. Airwallex (Malaysia) Sdn. Bhd., a company incorporated under the laws of Malaysia with company registration number 201801007747 (1269761-X), is regulated as a licensed remittance business under the Money Services Business Act 2011 (Licence number 00743 with an expiry date of 3 August 2028, an E-Money Issuer and a registered merchant acquirer under the Financial Services Act 2013.