In some countries, e-invoicing is becoming a legal requirement. This means businesses must issue and report invoices digitally to their tax authorities, often in real time.

If your country mandates e-invoicing, you can continue using Cliniko to manage appointments, patients, and billing while using a third-party software to handle the e-invoicing part.

One of the easiest ways to do this is by connecting Cliniko to Xero, our integrated accounting partner. From there, you can manage and submit e-invoices based on your country’s requirements.

In this guide, we'll cover:

An e-invoice is digital proof of a transaction between a supplier and a buyer and in many cases, is sent in real-time to a government tax system. It replaces paper or PDF invoices and is usually required for transactions between businesses (B2B), businesses and governments (B2G), and in some countries, businesses and consumers (B2C).

If you’re using Xero, you can manage e-invoicing processes directly from there. Xero meets both industry and region-specific requirements and uses Peppol for its e-invoicing network. Peppol is the framework that many governments, including Australia, New Zealand, United Kingdom, Singapore, and Malaysia have adopted for standardised e-invoicing.

Through the Cliniko-Xero integration, you'll be able to create and manage invoices and payments in Cliniko and have these automatically pushed to Xero.

Once the data is there, you can manage e-invoicing according to your local requirements. Any reporting, validation, and submission to tax authorities will be handled by Xero.

The steps to generate e-invoices may vary slightly depending on your country. Here are some Xero guides to help you get started -
Australia 🇦🇺: Send an eInvoice

New Zealand 🇳🇿: Send an eInvoice
UK 🇬🇧: Send an eInvoice
Singapore 🇸🇬: Send and receive invoices with e-invoicing

Malaysia is rolling out mandatory e-invoicing to all businesses in phases through its MyInvois system, run by the Inland Revenue Board of Malaysia (IRBM/LHDN).

Your deadline is dependent on your turnover. Here are the latest timelines as per the IRBM as of 5th June 2025:

How to generate e-invoices:

1. Use Cliniko + Xero

This involves creating your invoices in Cliniko, syncing them to Xero through our integration, and then managing your e-invoicing submissions there.

To get started:

Once the set up process is completed, you'll be able to send individual as well as monthly consolidated e-invoices to your customers and the IRBM from your Xero account if/when necessary.

We recommend getting in touch with Xero directly for questions about the set up or up-to-date instructions. If it helps, here are some guides from them that may be useful:
​Send individual e-Invoices to the IRBM
​Send self-billed e-Invoices to the IRBM
​Send consolidated e-Invoices to the IRBM

2. Use the MyInvois portal directly

Export invoice data from Cliniko and edit the CSV file to match the required fields before manually uploading it to IRBM's MyInvois portal to stay compliant. Here's a link to the MyInvois Portal User Guide for instructions.

3. Use another e-invoicing solution

You may also consider working with third-party accounting/tax/e-invoicing software though this may require more setup and manual work, as these are not integrated with Cliniko.

We’re actively exploring ways to better support compliance in the future, especially as e-invoicing becomes more common. With vastly different requirements between countries, we’re currently focused on improving our integration with platforms like Xero that already offer e-invoicing support.

If we introduce new features or integrations, we’ll be sure to let you know.

It's important to always check with your local tax authority or accounting software to ensure you’re meeting all current e-invoicing requirements. If you’re unsure what steps to take, feel free to reach out. We’ll help guide you in the right direction. 💬