Shopify Malaysia: Payment Gateway Problems You Should Know

Disclaimer: This article is for informational and educational purposes only. It does not constitute financial, legal, compliance, or technical advice. References to any brands or gateways do not imply endorsement unless stated otherwise.

Shopify Pay and Malaysian Retailers

Shopify has become one of the most popular e-commerce platforms in Malaysia. Its appeal lies in its ease of use, wide selection of themes, a large app ecosystem, and the ability to scale from small home-based brands to full retail chains. However, while Shopify is designed as a global platform, its payment ecosystem is not fully aligned with the needs of Malaysian retailers.

The most common Shopify challenge in Malaysia relates to payment gateways. Merchants often face issues like limited support for local payment methods, cross-border settlement fees, slower payout cycles, and occasional technical compatibility problems. These hurdles can affect cash flow and create a less smooth checkout experience for customers. 

This comprehensive guide explains how Shopify payments work, the Shopify problem Malaysian retailers commonly face, the consequences of these issues, and practical solutions to ensure smoother payment acceptance. 

Shopify Payment Gateway Features

Shopify provides several built-in and integrable payment features designed to provide secure, efficient online transactions. For Malaysia-based retailers, it is important to understand which features are available locally and which require specific conditions.

Shopify Payment Features

Secure Checkout Page Hosted on Shopify

• Payment Card Industry Data Security Standard (PCI DSS)-compliant, hosted checkout that integrates with approved payment providers.
• Consistent user experience managed by Shopify’s checkout framework.
• Works with direct/embedded or external/hosted gateways based on provider.

Fraud Analysis Tools

• Designed primarily for online card orders where Shopify can verify payment data.
• Richer risk signals and recommendations are available with eligible processors.
• Merchants should still run operational reviews for local non-card methods.

Multi-Currency Checkout (Conditional)

• Native multi-currency checkout typically requires Shopify Payments.
• Shopify Payments is not available to stores based in Malaysia.
• Malaysian stores can show converted prices via apps, but checkout occurs in the store currency.

Credit and Debit Card Acceptance via Third-Party Providers

• Malaysia-based stores can enable card payments through compatible third-party gateways.
• Provider terms, fees, fraud tooling, and payout timelines vary.
• Test card flows on mobile to validate 3D Secure (3DS) protocols and post-payment status updates.

Compatibility with Selected Third-Party Gateways

• Supports direct/embedded or external/hosted integrations depending on provider.
• External redirects add steps; embedded methods reduce friction.
• Confirm webhook configuration and reliability for order status updates (paid/pending/failed).

Taxes and Shipping

• Shopify supports tax and shipping setups globally, but deeper automation is region-limited.
• Discounted label buying via Shopify Shipping focuses on the United States, Canada, and Australia.
• Malaysian merchants typically configure taxes and courier rates manually or via apps.

Subscriptions and Recurring Billing (Conditional)

• Subscriptions work only with specific supported gateways (e.g., Shopify Payments).
• Local rails are generally not usable to purchase subscriptions.
• Availability and compliance vary by region, be sure to validate before launching.

Manual Payment Methods

• Manual bank deposit/transfer is available as an offline option.
• Not instant; merchants need to manually mark orders as paid once funds are verified.
• Useful for B2B or high-value orders but requires clear reconciliation SOPs.

(Source: Shopify)

Common Issues With Shopify Payment Gateways

Malaysia’s retail landscape is heavily influenced by local payment behaviour. Many shoppers prefer QR transactions, fast bank transfers, and local wallets routed through national payment rails. When default payment coverage does not fully align with these expectations, several Shopify problems arise. (Source: PayNet; Bank Negara Malaysia)

1. Limited Local Payment Options

Shopify does not provide built-in instant support for most Malaysian-first payment rails. Retailers often discover that:

• QR-based payments such as DuitNow QR require third-party gateways or apps.
• FPX online banking payments are not provided natively and must be enabled through third-party gateways or apps.
• Manual bank deposit exists but is offline and not instant, requiring manual reconciliation.

This creates friction for customers who prefer paying through familiar local methods and can lead to cart abandonment when preferred options are missing. (Source: PayNet; Shopify)

2. Foreign Currency Settlement Problems

Because Malaysia-based stores rely on third-party providers rather than the Shopify Payment Gateway, settlement currencies and banking arrangements vary by gateway. Some providers settle in MYR, while others settle in foreign currencies. This can lead to:

• Exposure to exchange rate fluctuations
• Conversion fees and reconciliation differences
• Inconsistent payout values that complicate cash flow planning

These risks are material for SMEs that operate on tight margins. (Source: Shopify)

3. Delayed Settlement and Payout Cycles

Local businesses that rely on fast cash rotation may struggle with:

• Extended payout windows set by external providers
• Settlement delays during peak seasons
• Unpredictable timelines when cross-border processes are involved

Delays affect working capital, vendor payments, and inventory replenishment cycles. (Source: Shopify)

4. Higher Transaction and Cross-Border Fees

When Malaysian stores use third-party providers, fees can be higher due to:

• International routing or foreign settlement
• Currency conversion
• Shopify third-party transaction fees for external gateways

These costs directly reduce retailer margins, especially in low-ticket or high-volume models. (Source: Shopify)

5. Integration Conflicts and Plugin Errors

Retailers may encounter technical challenges when combining apps and payment plugins, such as:

• Redirect loops or session expiries during checkout with external/hosted flows
• Conflicts between multiple apps that modify the cart or checkout
• Broken buttons or API instability leading to failed transactions

These problems are not universal but are common enough to warrant preventive setup and testing. (Source: Shopify)

6. Checkout Redirects That Increase Abandonment

Some third-party gateways redirect customers away from Shopify’s checkout page to a hosted page. Redirects can:

• Add steps and slow the process
• Reduce trust due to a change of domain or design
• Increase drop-offs, especially on mobile networks
• Confuse first-time online shoppers

Independent performance studies consistently show that even small delays and extra steps increase bounce and reduce conversion. (Source: Think with Google; Akamai)

Consequences of These Shopify Payment Gateway Issues

A Shopify problem that affects payment will affect far more than technical workflow. It also has direct consequences on sales, trust, and long-term performance.

1. Higher Cart Abandonment Rates

Customers abandon checkout when:

• Their preferred local payment method is unavailable
• They encounter redirects and additional steps
• Checkout fails or times out on mobile

Friction at the payment stage is one of the biggest reasons for lost revenue in Malaysian e-commerce. (Source: Think with Google; Akamai)

2. Reduced Customer Trust

Security, familiarity, and convenience heavily influence Malaysian online shoppers. When payment pages look unfamiliar or require redirection, many customers hesitate or leave. Consistent branding and clear messaging help mitigate this risk. (Source: Think with Google)

3. Cash Flow Instability

Delayed settlement harms everyday operations, including:

• Supplier payments
• Staff payroll
• Inventory restocking
• Scaling efforts
• Campaign launch timing

Retail growth slows when payouts are unpredictable. (Source: Shopify)

4. Increased Operational Costs

Payment issues add unnecessary expenses such as:

• Cross-border and conversion fees
• Longer reconciliation time due to currency mismatches
• Errors in payout reporting across providers
• Additional customer support workload for failed or pending payments

These costs accumulate and reduce profitability. (Source: Shopify)

5. Difficulty Scaling the Business

Without reliable, locally aligned payment acceptance, merchants struggle to:

• Increase marketing spend confidently
• Manage high order volumes during campaigns
• Expand internationally with clean currency operations
• Enter new product categories without payment-flow risk

A store with unstable payment processing cannot grow sustainably. (Source: Shopify)

How These Issues Can Be Solved

Malaysian retailers do not need to abandon Shopify. Instead, they can apply practical solutions to fix or minimise a Shopify problem with payment gateways.

1. Integrate a Malaysian-Friendly Third-Party Gateway

Choose a provider that supports:

• Ringgit-based settlements
• DuitNow QR acceptance
• FPX online banking
• Compliance with Malaysian payment regulations

This ensures better alignment with customer expectations and more predictable payouts. (Source: PayNet; Bank Negara Malaysia)

Implementation notes:

• Verify that order status updates (paid, pending, failed) are pushed back to Shopify via reliable webhooks.
• Check whether the provider offers embedded/direct checkout to reduce redirects and improve conversion.
• Align the provider’s settlement timeline with your cash flow needs. (Source: Shopify; PayNet)

2. Optimise Shopify’s Checkout Configuration

Retailers can:

• Prefer direct or embedded payment methods to reduce steps versus external redirects
• Remove or reconfigure conflicting apps that alter the cart or checkout
• Enable dynamic checkout buttons only where they do not conflict with payment options
• Test mobile performance thoroughly to keep pages light and fast

A smoother, faster checkout improves conversion significantly. (Source: Shopify; Think with Google; Akamai)

3. Provide Multiple Payment Options

Offering more than one method gives customers flexibility. Retailers can add:

• DuitNow QR for QR payments
• FPX for instant bank transfers
• Select digital wallets through compatible gateways
• Card payments for customers who prefer them

This ensures that every customer has a familiar way to pay. (Source: PayNet)

4. Adjust Currency Settings Properly

Align settlement currency with store currency wherever possible to minimise:

• Double conversion fees
• Exchange rate volatility between authorisation and payout
• Reconciliation errors across bank accounts

Because multi-currency checkout requires Shopify Payment Gateway and is not available for Malaysia-based stores, clarity on displayed versus charged currency is essential. (Source: Shopify)

5. Use Reliable Apps for Local Payment Extensions

Apps and integrations built for Malaysian merchants can bridge local payment rails while maintaining Shopify compatibility. Prioritise solutions with:

• Clear documentation
• Strong merchant reviews
• Transparent settlement timelines
• Support channels suited to Malaysian time zones

This reduces operational risk and simplifies support during peak sales periods. (Source: Shopify; PayNet)

6. Improve Customer Communication

Reduce payment failure confusion by:

• Showing accepted payment method icons clearly on product and cart pages
• Adding a “How to Pay” section for QR and FPX flows
• Explaining any redirects before the payment step
• Offering live chat or a hotline during campaign periods

Better communication reduces checkout anxiety and improves completion rates. (Source: Shopify)

7. Consider a Secure External Checkout Page for Specific Use Cases

Some retailers choose a carefully managed external checkout to gain:

• Broader local method coverage
• Faster settlement in MYR
• Better performance during large campaigns
• Operational control with provider-level dashboards

If you use this approach, test thoroughly on mobile and maintain consistent branding to mitigate trust loss from redirection. (Source: Shopify; Think with Google; Akamai)

Conclusion

Shopify remains a powerful and versatile platform for Malaysian retailers, but payment gateway restrictions continue to create challenges in reliability, customer experience, and settlement speed. By understanding these limitations, retailers can take proactive steps to optimise checkout flow, solve settlement issues, and provide payment options that Malaysian customers trust. 

Implement the fixes in this guide to reduce redirects, add the right local methods, clarify currency handling, and streamline reconciliation.

For retailers that want a dependable, secure, and localised all in one payment solution, we provide scalable and compliant systems that integrate smoothly with online stores. Explore more on our services to see what suits you best today, and improve your retail performance!