10 Best E-Invoicing Software in Malaysia

Managing invoices can be one of the most time-consuming challenges for growing companies. This is where E-Invoicing Software shows its value by simplifying the way businesses create, send, and track invoices through a secure digital system.

Unlike traditional invoices, electronic invoices minimize errors, accelerate payment cycles, and provide finance teams with clear, real-time insights into cash flow.

For visionary executives, this is not just a tool but a strategy to enhance compliance, efficiency, and profitability. After thorough research and direct reviews, I have compiled the top 10 e-invoicing software solutions in Malaysia to help you choose the right one.

Keep reading, as the right solution can transform how your company manages billing and strengthen its competitive edge.

What is E-Invoicing Software?

E-Invoicing Software is a digital solution that enables companies to issue, send, and receive invoices in a structured electronic format, rather than as simple PDFs or paper documents.

Unlike basic invoicing tools, e-invoicing connects directly with accounting systems, tax authorities, or payment platforms, allowing data to flow automatically without manual input.

This not only reduces errors but also speeds up payment processes and ensures compliance with financial regulations. For businesses, it means greater efficiency, transparency, and control over the entire billing cycle.

E-Invoicing vs Invoicing Software

When discussing digital invoicing, it’s essential to clarify the difference between traditional invoicing software and e-invoicing software. While both aim to simplify billing, they are not the same. Invoicing software focuses on creating and sending invoices in digital formats like PDF or Word.

In contrast, e-invoicing software goes further by delivering invoices in a structured electronic format that other systems can automatically process. The table below highlights the key distinctions to help your company see where e-invoicing delivers greater value.

Why do Businesses Need E-Invoicing Software?

Managing invoices may look simple on the surface, but for many companies it quickly becomes a source of inefficiency and frustration. Delayed payments, manual errors, and compliance risks often hold back finance teams from focusing on more strategic work.

This is where e-invoicing software creates real impact. By moving from traditional invoicing methods to a fully digital and automated system, businesses can eliminate unnecessary pain points and unlock new levels of efficiency. Businesses need e-invoicing software because it helps them:

• Save time and resources by automating invoice creation, delivery, and tracking
• Reduce costly errors with built-in validation and standardized formats.
• Accelerate cash flow through faster approvals and integrated payment options.
• Gain real-time visibility into invoice status and financial performance.
• Stay compliant with tax regulations and industry requirements effortlessly.

10 Recommendations for the Best E-Invoicing Software

With a clear understanding of what e-invoicing software is and why it matters for your business, the next step is choosing the right solution. To help you make an informed decision, we’ve reviewed and shortlisted the ten best e-invoicing software options in Malaysia that stand out for their features, reliability, and value for companies like yours.

Below, you will find our curated list of the best e-invoicing software in Malaysia, designed to support companies in achieving greater efficiency, accuracy, and compliance.

1. HashMicro Best E-Invoicing Software

HashMicro has established itself as one of Southeast Asia’s most trusted ERP providers, supporting thousands of companies across sectors such as retail, manufacturing, construction, and professional services.

Known for its modular cloud-based solutions, the company empowers businesses to streamline complex processes into a single, integrated system that enhances efficiency and control.

Its e-invoicing software is a core part of this ecosystem, enabling companies to automate invoice creation, validation, and submission while maintaining compliance with Malaysia’s tax regulations.

The platform is fully Peppol-ready and connects seamlessly with LHDN, ensuring secure, real-time invoice exchanges. With features such as customizable templates, payment link integration, and advanced analytics dashboards, HashMicro helps finance teams reduce errors, accelerate collections, and gain complete visibility over cash flow.

Key features:

• Tax Invoice Serial Number: Assigns a unique serial number to each tax invoice, ensuring traceability and compliance with Malaysia’s tax regulations.
• Generate Tax Invoice Serial Number: Automatically generates serial numbers for every new tax invoice, reducing manual work and eliminating the risk of duplication or human error.
• Output and Input VAT: Records both sales tax (output VAT) and purchase tax (input VAT) accurately, giving businesses a clear view of their tax liabilities and claims.
• Aggregated Output and Input VAT: Consolidates all VAT records into a single report, simplifying reconciliation and making it easier for finance teams to prepare tax filings.
• Export Product: Allows companies to export detailed product information linked to invoices, ensuring accurate reporting and smooth cross-border transactions.
• Export Partner: Provides the ability to export partner or client data associated with invoices, improving transparency and facilitating compliance checks.

2. Xero E-Invoicing Software Malaysia

Xero is a globally recognized cloud-based accounting platform that has gained substantial traction in Malaysia for its reliable e-invoicing capabilities. Designed to support businesses of all sizes, Xero simplifies the invoicing process while ensuring compliance with local tax requirements.

Many companies choose Xero because it is user-friendly, integrates smoothly with other business tools, and helps finance teams save time on manual tasks.

Its reputation for accessibility and scalability makes it a trusted option for companies looking to streamline financial operations and strengthen cash flow management.

Key features:

• Online Invoicing
• Bank Connections
• Expense Management
• Multi-Currency Accounting

3. Refrens E-Invoicing Software

Refrens is a trusted cloud-based platform used by thousands of businesses worldwide, including many in Malaysia. Known for its simplicity and affordability, it helps companies streamline invoicing while staying compliant with local regulations.

Its intuitive design and flexibility make it especially popular among SMEs and growing businesses looking for an efficient way to manage billing and financial processes.

Key features:

• Bulk e-Invoice Generation
• Smart Data Validation & Error Checking
• GSTR and e-Invoice Reports

4. QuickBooks E-invoicing Software Malaysia

QuickBooks is a leading cloud-based accounting platform trusted by businesses worldwide and widely adopted in Malaysia. Its e-invoicing solution is fully compliant with LHDN requirements, helping companies issue and manage invoices according to local tax regulations.

With its user-friendly design and focus on compliance, QuickBooks makes it easier for businesses to streamline invoicing and stay efficient while meeting Malaysia’s e-invoicing mandate.

Key features:

• Multi-Currency Support
• Mobile Accessibility
• Custom Invoicing

5. Bukku E-Invoice Malaysia

Bukku is a fast-growing e invoice Malaysia, particularly favoured by small and medium-sized businesses.

Its e-invoicing solution is fully compliant with LHDN’s MyInvois system and supports seamless integration with the Peppol network, helping companies meet regulatory requirements without disrupting existing workflows.

Key features:

• Consolidated E-Invoice Submission
• Self-Billed E-Invoice Submission
• Cancelling an E-Invoice

6. Invoice2go Software Malaysia

Invoice2go is a mobile-first cloud invoicing solution widely used by small and micro businesses around the globe, and its accessibility makes it a viable option for Malaysian companies. Users appreciate Invoice2go for its simplicity, mobile flexibility, and intuitive interface, which helps streamline billing even for teams that operate on the go.

Its ease of use and focus on essential invoicing needs make it an attractive choice for businesses seeking a fast, hassle-free invoicing experience.

Key features:

• Invoice Tracking
• Online Payments
• Invoice Creation & Customization

7. QNE AI Cloud Accounting

QNE AI Cloud Accounting is a trusted cloud-based solution in Malaysia that supports compliance with LHDN’s e-invoicing requirements. AI-driven tools help businesses streamline financial processes, improve accuracy, and work flexibly from anywhere.

Its user-friendly design makes it a reliable choice for companies aiming to modernize invoicing with confidence.

Key features:

• Compliance-Driven AI
• Optical Character Recognition (OCR)
• E-Invoice Management

8. AutoCount E-Invoicing Software

AutoCount is a reliable invoicing software that helps businesses manage billing efficiently and accurately. Its smooth integration with existing systems and consistent performance make it a practical choice for companies seeking ease of use in their financial operations.

Key features:

• Auto-Submission
• Auto-Check Status
• Auto-Sync

9. InvoisPro E Invoicing Software

InvoisPro is an AI-powered e-invoicing platform designed to help Malaysian businesses comply seamlessly with regulatory requirements. Built to simplify complex invoicing processes, it offers a scalable solution that suits both small and large companies.

One of its key strengths lies in providing businesses with a reliable and user-friendly system that ensures compliance while also supporting efficiency in day-to-day operations.

Key features:

• AI-Powered Automation
• Affordable Accounting Integration
• Quick & Simple Onboarding

10. Aspert’s AiNexus

Aspert’s AiNexus is a Malaysian-developed e-invoicing solution designed to help businesses transition smoothly into digital invoicing. It emphasizes compliance with local regulations while offering a straightforward and reliable platform that reduces manual work and supports better financial management.

Its practical approach makes AiNexus a solid option for companies looking to modernize their invoicing processes with confidence.

Key features:

• ERP Integration
• Tax Compliance

Conclusion

Selecting the appropriate e-invoicing software is pivotal for businesses aiming to enhance operational efficiency and ensure compliance with regulatory standards.

Among the top solutions available, HashMicro’s E-Invoicing Software distinguishes itself by offering seamless integration with the Peppol network, facilitating automated invoice generation, and ensuring adherence to global standards.

For businesses seeking to streamline their invoicing processes, HashMicro provides a comprehensive solution tailored to meet diverse needs. Explore its capabilities firsthand by requesting a free demo, allowing you to assess its suitability for your business requirements.

FAQ E Invoicing Software

• Is e-invoicing mandatory in Malaysia?

  E-Invoicing in Malaysia has been mandated by the Inland Revenue Board of Malaysia (LHDN) since August 2024. Under this mandate, all businesses are required to issue and receive electronic invoices in real time, following the prescribed format.

• How much to charge for invoicing?

  The cost of invoice processing varies, but most businesses spend between $15 and $40 per invoice. To get to the lower end of the spectrum, review the elements that can impact invoice costs and streamline your accounts payable. Remember that your costs will vary depending on the type of invoice you’re using.

• How to calculate the invoice amount?

  Add in any applicable taxes on those goods and services. Subtract any discounts offered to the customer and any instalments the customer has already paid. The calculation will look like this: (invoice items + tax) – (discounts + instalments) = invoice amount.