Best Accounting Software for Medical Practices Australia 2026
Last updated: March 2026 · Prices verified from official AU vendor sites · Affiliate disclosure
Xero is the best accounting software for Australian medical and allied health practices. It integrates directly with Cliniko, Nookal, Halaxy, Power Diary, and virtually every practice management platform used in Australia. Patient billing, Medicare reconciliation, and practitioner payments all connect without manual data entry. MYOB is rarely the right choice here unless you have complex inventory or payroll Award obligations.
Best for medical practices - comparison
| Software | Price/mo | Verdict | Key integrations |
|---|---|---|---|
| Xero | From $37 | Best overall | Cliniko, Nookal, Halaxy, Power Diary, HotDoc |
| MYOB | From $31.82 | For complex payroll only | Limited practice management integrations |
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Cliniko integration syncs invoices and payments to Xero automatically - no manual data entry between systems. Nookal, Halaxy, and Power Diary all integrate directly as well, so whatever practice management platform you use, Xero almost certainly connects to it. Xero also handles practitioner payroll correctly (employees or contractors, with correct super and PAYG handling), GST-exempt income coding for health services, and integrates with NDIS management platforms if your practice provides disability supports.
Common questions
Is health income GST-free in Australia?
Most human health services are GST-free under Australian tax law - including medical, dental, physiotherapy, psychology, and many allied health services. Some services may be taxable (certain cosmetic procedures, some allied health services). Your accountant should set up the correct GST codes for your specific services in Xero.
Does Xero integrate with Cliniko?
Yes - directly. The Cliniko-Xero integration syncs invoices, payments, and practitioners automatically. You can set it to sync in real time or on a schedule. It handles both individual and bulk billing scenarios.
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Start your free trial →See also: NDIS accounting software · Best accounting software AU · Xero review
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