Halaxy Xero Integration Guide [2026 Updated]

Connecting your practice management software directly to your accounting system is one of the most effective ways to reduce administrative work. For healthcare professionals using Halaxy for patient management and Xero for their books, a direct integration bridges the gap between clinical operations and financial tracking. This guide walks you through the step-by-step process of setting up the integration, explains what data syncs, and provides solutions for common issues you might encounter.

Why Connect Halaxy and Xero?

Manually entering invoice and payment details from your practice management software into your accounting platform is not only time-consuming but also prone to error. A single misplaced decimal or an overlooked invoice can throw off your entire financial reporting. The primary benefit of integrating Halaxy with Xero is automation. It creates a direct channel where key financial data flows from one system to the other without manual intervention.

This connection accomplishes several key goals for your practice:

• Saves Administrative Time: It eliminates the double-entry of invoices and payments. When you issue an invoice in Halaxy, it automatically appears in Xero. When a payment is recorded, it's reflected in both systems, drastically cutting down on bookkeeping hours.
• Improves Financial Accuracy: Automation removes the risk of human error from manual data entry. This ensures your revenue figures, accounts receivable, and payment records are consistent and accurate, giving you a reliable picture of your practice's financial health.
• Simplifies Bank Reconciliation: With payments from Halaxy flowing directly into Xero, matching them with deposits in your bank feed becomes much simpler. This makes your monthly reconciliation process faster and less stressful.
• Provides a Centralized Financial View: Your practice's billing happens in Halaxy, but your overall business finances—including expenses, payroll, and liabilities—are managed in Xero. The integration consolidates all your revenue data into your central accounting ledger, providing you and your accountant with a comprehensive, up-to-date view of business performance.

What You Need Before You Start

Before beginning the setup process, a little preparation will ensure everything goes smoothly. Make sure you have the following ready:

• An Active Halaxy Account: You need an active Halaxy subscription. Importantly, you must have administrator or owner-level access to access and configure integration settings.
• An Active Xero Account: You will also need an active Xero subscription. Just like with Halaxy, you must have 'Standard' or 'Adviser' user permissions to authorize and configure application connections.
• Login Credentials: Have the correct username and password handy for both your Halaxy and Xero accounts. The authorization process will require you to log into both platforms.
• A Clear Chart of Accounts: Before you connect the two systems, it’s a good idea to review your Chart of Accounts in Xero. Know which revenue accounts you want Halaxy invoices to post to and which bank accounts you’ll use for mapping payments. This will make the configuration step much clearer.

Step-by-Step Guide to the Native Halaxy and Xero Integration

Halaxy provides a native, or built-in, integration with Xero designed for straightforward setup. Follow these steps carefully to establish the connection and configure your synchronization settings.

Step 1: Locate the Integration Settings in Halaxy

First, log in to your Halaxy account. Once you are in your dashboard, navigate to the main settings area. From there, find the section dedicated to integrations, add-ons, or third-party applications. Look for the Xero logo or an option explicitly labeled "Xero Integration" and select it to begin the setup process.

Step 2: Authorize Halaxy to Connect to Xero

You will now see an option to connect to Xero, typically a button that says "Connect" or "Authorize." Clicking this will redirect you to the Xero login page. Enter your Xero email and password. Xero will then ask you to grant Halaxy permission to access your organization's data. Review the permissions—they generally allow Halaxy to create and update invoices, payments, and contacts. Select the correct Xero organization if you manage more than one, and click "Allow Access." You will then be redirected back to Halaxy.

Step 3: Configure Your Synchronization Settings

This is the most important step, as it determines how data flows between the two systems. Take your time to map your Halaxy data to the correct places in Xero.

• Account Mapping: You need to tell Halaxy where to send its financial information. Map your Halaxy revenue streams (e.g., consultation fees, product sales) to the corresponding sales/revenue accounts in your Xero Chart of Accounts.
• Payment Mapping: Link the payment methods in Halaxy (e.g., Credit Card, Cash, Direct Deposit) to the appropriate bank or clearing accounts in Xero. For example, all payments made via your clinic’s terminal should be mapped to your main business checking account in Xero.
• Tax Mapping: Ensure that the tax rates you use in Halaxy (such as GST or VAT, if applicable) are correctly matched to the corresponding tax rates in Xero. This is essential for accurate tax reporting.
• Invoice Status Selection: Decide how invoices from Halaxy should appear in Xero. You can often choose to send them over as a Draft, Awaiting Approval, or automatically Approved. Sending as Draft or Awaiting Approval is a safe default, as it allows for a final review in Xero before the transaction is finalized.

Step 4: Run an Initial Sync and Test the Connection

After your settings are configured, it's time to test the link. Find a recently created invoice in Halaxy or create a new test invoice. Initiate a manual sync (there is often a "Sync Now" button). Once a sync is complete, log into your Xero account. Navigate to the sales invoices section and look for the test invoice. Check that:

• The customer name, invoice number, and date are correct.
• The line items and amounts match the Halaxy invoice.
• The correct sales account and tax rate were applied.

Next, record a payment against that invoice in Halaxy and run the sync again. Verify that the payment appears correctly in Xero and is applied to the invoice.

Step 5: Activate Automatic Syncing

Once you are confident that data is flowing correctly, you can enable automatic synchronization. The integration will typically run syncs at set intervals, such as every hour or once nightly. Activate this feature to ensure your accounts are always kept up-to-date with minimal manual effort. Remember to periodically monitor the integration from Halaxy’s settings page to check for any sync errors.

What Data Syncs Between Halaxy and Xero (and What Doesn’t)?

Understanding the scope of the integration helps manage expectations and establish correct workflows. Here is a breakdown of the typical data transfer:

• Invoices: This is the core of the integration. New invoices and credit notes created in Halaxy are pushed to Xero. Updates to existing invoices in Halaxy should also sync across.
• Payments: When you record a payment against an invoice in Halaxy, that payment information is sent to Xero and applied to the corresponding invoice. This is key for easy reconciliation.
• Practice Expenses: Any expenses you record within Halaxy can be mapped and synced to the appropriate expense accounts in Xero, helping to consolidate your financial data.
• Contacts: Patient financial information needed for invoicing is synced, creating or matching with contacts in Xero.

It's equally important to know what information doesn’t sync:

• Clinical Notes & Patient Records: All sensitive patient health information remains securely within Halaxy. The integration only deals with financial data.
• Appointments and Calendars: Schedulers and appointment data are part of practice management and do not sync to Xero.
• Templates and Forms: Practice-specific templates and forms remain exclusively in Halaxy.

Common Problems and How to Fix Them

Even with a good setup, you may occasionally run into issues. Here are fixes for the most common problems:

• Authorization Errors or a Failed Connection: This usually happens if a password has been changed or if the connection token has expired for security reasons. The fix is simple: Go back to the integration settings in Halaxy, disconnect the Xero integration, and then walk through the authorization process again to re-establish a fresh, secure link.
• Data Mismatches or Missing Information: If invoices appear in Xero with the wrong revenue account or tax rate, the issue is almost always in the mapping configuration. Return to the sync settings and carefully review your account, payment, and tax mappings. Ensure every item in Halaxy has a designated destination in Xero.
• Sync Delays: Remember that most integrations of this type do not sync in real-time. Before assuming an error, check the sync frequency (e.g., hourly). If you need data transferred immediately, use the "Sync Now" or "Run Manual Sync" option.
• Duplicate Entries: Duplicates typically arise from a workflow problem, not a sync error. For example, if you create an invoice in Halaxy which syncs to Xero, and then someone on your team manually creates the same invoice in Xero, you'll have a duplicate. The rule is simple: all billing and invoicing must originate in Halaxy. Xero should be the destination, not the starting point, for any transaction synced from your practice management software.

Beyond the Native Integration: Zapier and Custom Workflows

For most practices, the native Halaxy-Xero integration is more than sufficient. However, if you need more complex, customized automation, a third-party connector tool like Zapier can be useful. For example, if you wanted a new paid invoice in Halaxy to trigger a specific sequence of events—like creating an entry in Xero, adding the patient to a specific email list for a follow-up, and sending a notification to your practice manager—Zapier could build that multi-step workflow. This route requires more technical setup but offers immense flexibility if your operational needs go beyond simple financial syncing.

Final Thoughts

Integrating Halaxy and Xero is a practical move to connect your clinical and financial operations, reducing administrative overhead and ensuring your financial records are accurate. By following a structured setup and understanding how the data flows, you create a more efficient workflow for your entire practice.

Keeping your practice financially healthy also requires a deep understanding of tax regulations. When you or your accountant face complex tax questions related to things like revenue recognition, expense deductibility, or state compliance, Feather AI can help. We provide instant, citation-backed answers drawn directly from authoritative sources like the IRC and IRS guidance, helping your trusted financial advisors get the clarity they need in seconds.