Bookkeeping for medical practices, AustraliaA dedicated, university-qualified graduate accountant reconciles Medicare, health fund and patient receipts against your practice software, codes GST-free and other income separately, prepares payroll and super, and has BAS figures ready for your registered BAS or tax agent. Your bookkeeper is based in the Philippines and works in your Xero, MYOB or QuickBooks file during Australian business hours.
GST in a medical practice
A medical service is GST-free when a Medicare benefit is payable for it, or when it is supplied by or on behalf of a medical practitioner and is generally accepted in the medical profession as necessary for the appropriate treatment of the patient (ATO, Medical services).
Other health services are GST-free when the service is on the ATO's list of health services, is performed by a recognised professional in that service, and is generally accepted in that profession as necessary for the appropriate treatment of the patient (ATO, Other health services).
| Income | General rule | Reason given by the ATO |
|---|---|---|
| Consultation for which a Medicare benefit is payable | GST-free | A Medicare benefit is payable for the service |
| Treatment by a practice nurse on behalf of the treating doctor | GST-free | Performed on behalf of a medical practitioner as part of the practitioner's service |
| Listed health services such as physiotherapy, psychology, podiatry and dental | GST-free when the conditions are met | Listed service, recognised professional, necessary for appropriate treatment |
| Cosmetic procedure where no Medicare benefit is payable | Not GST-free | ATO example: removal of a tattoo |
| Report for an insurer or for litigation where no Medicare benefit is payable | Not GST-free | The recipient is not the patient and the report is not a natural part of a GST-free service |
| Remedial massage | Not GST-free | Not a listed health service |
General rules from the ATO's GST and health guide, last updated by the ATO on 12 June 2024 and checked on 29 September 2026. How a particular service is treated depends on its facts. Your registered tax or BAS agent decides the treatment for your practice. Your bookkeeper codes each income type the way your agent has set it up, so GST-free and other income are reported separately on the BAS.
What the books of a practice involve
The work is ordinary bookkeeping with six features that are particular to health.
Medicare, private health fund, DVA, workers compensation and NDIS payments arrive in batches that rarely match a single invoice. Each deposit is reconciled against the billing report from your practice software.
Most consultation income is GST-free. Cosmetic work and reports for insurers usually are not. Each income type is coded separately so the BAS shows the right mix.
Practices engage practitioners as employees, as contractors, or under service agreements. How an arrangement is classified is a matter for your accountant or lawyer. Your bookkeeper records each one consistently.
Nurses are generally covered by the Nurses Award 2020 (MA000034). Allied health and support staff are generally covered by the Health Professionals and Support Services Award 2020 (MA000027). Pay runs are prepared from the classifications your practice has set.
For earnings paid from 1 July 2026, super must be received by each employee's fund within 7 business days of payday. Super is prepared with every pay run.
Monthly profit and loss, balance sheet and cash flow, with fee income by practitioner where your practice software reports it.
What is handled
One person working in your accounting software, alongside the practice system your front desk already uses.
Medicare, health fund and patient payments matched to the billing report on a set cycle, with differences listed for follow-up.
GST-free and other income coded separately, following the treatment your registered agent has set.
Pay runs, Single Touch Payroll reports and super payments prepared for your approval.
Medical supplies, rent, equipment leases and locum invoices captured, coded and scheduled for payment.
BAS figures and workpapers prepared each quarter for your registered BAS or tax agent to review and lodge.
Profit and loss, balance sheet and cash flow for the month just finished.
Get in touch
Tell us a little about your business and what you need looked after. We reply within one business day, Australia-wide, and fifteen minutes on the phone is enough to say whether a dedicated bookkeeper suits you and what it would cost.
Prefer to talk? 1300 66 88 14
Practice management software
Practice management systems such as Best Practice, MedicalDirector, Genie, Cliniko and Halaxy handle appointments, billing and claims. Your bookkeeper does not replace them and does not need to work in them every day.
Billing and banking reports from the practice system are used to keep Xero, MYOB or QuickBooks reconciled. Bookkeeping uses financial reports. It does not need access to clinical notes.
Billing and banking reports exported on the cycle you choose.
Xero, MYOB, QuickBooks or Reckon, whichever the practice already uses.
Receipts, bills, payroll and bank data. Clinical records stay in the practice system.
User permissions set by you, removable by you, with a signed NDA in place.
Your bookkeeper is a university-qualified graduate accountant with Australian experience, employed by FreeMyCloud and based in our Manila office. The same person works on your file every day and is ready to start within three business days.
FreeMyCloud is Australian owned and was founded in 2010, with offices in Melbourne and Manila.
A dedicated FreeMyCloud bookkeeper typically costs 50 to 70% less than a local equivalent. The figure for your practice depends on hours and transaction volume.
Getting started
Four steps, with no change to your practice software or your front desk routine.
You describe the practice, the billing mix, the software and the payroll.
We match a graduate accountant to your software and workload.
The NDA is signed and you invite your bookkeeper into your accounting file.
Receipts reconciled every week, reports every month, BAS figures every quarter.
Guides for health practices
FreeMyCloud provides bookkeeping for medical practices in every state and territory: GP clinics, specialist practices, medical centres, allied health practices and multi-disciplinary clinics, from individual practitioners to groups with several sites.
A practice receives income from Medicare, private health funds, DVA, workers compensation insurers, the NDIS and patients directly. Each payer remits on its own timetable and in its own format, which is why receipts reconciliation takes more time in a practice than in most businesses of the same size.
Dental clinics have their own page. See bookkeeping for dental clinics.
Frequently asked questions
A bookkeeper for a medical practice reconciles Medicare, health fund and patient receipts against the practice billing report, codes GST-free and other income separately, enters supplier bills, prepares pay runs and super, and produces monthly reports. Each quarter the BAS figures are prepared for a registered BAS or tax agent to review and lodge.
A medical service is GST-free when a Medicare benefit is payable for it, or when it is supplied by or on behalf of a medical practitioner and is generally accepted as necessary for the appropriate treatment of the patient. Cosmetic procedures with no Medicare benefit, and reports for insurers or litigation, are not GST-free. The rules are in the ATO's GST and health guide.
Nurses are generally covered by the Nurses Award 2020 (MA000034). Allied health professionals and support staff are generally covered by the Health Professionals and Support Services Award 2020 (MA000027). Which award and classification applies to a particular employee depends on the role, and the Fair Work Ombudsman can confirm coverage.
For earnings paid from 1 July 2026, the super guarantee contribution must be received by the employee's fund within 7 business days of payday. Super is prepared with every pay run instead of once a quarter. Our Payday Super guide covers the detail.
Bookkeeping uses financial records: billing and banking reports, supplier bills, payroll and bank data. It does not need access to clinical notes. Your bookkeeper works in your accounting file at the permission level you choose, under a signed non-disclosure agreement.
A dedicated FreeMyCloud bookkeeper typically costs 50 to 70% less than a local equivalent, with no setup fee and no lock-in contract. The figure depends on the hours and transaction volume your practice needs. The cost page explains how it is worked out.
FreeMyCloud bookkeepers are able to work with Xero, MYOB, QuickBooks and Reckon, using billing and banking reports from practice systems such as Best Practice, MedicalDirector, Genie, Cliniko and Halaxy. There is no need to change the software you already use.
Most clients are running within three business days of the first call. The steps are a 30-minute call, matching a bookkeeper to your software and workload, signing the NDA and inviting your bookkeeper into your accounting file.
This page is general information about Australian bookkeeping and reporting obligations, current as at 29 September 2026. It is not tax, financial or legal advice. FreeMyCloud is not a registered tax agent and does not prepare or lodge tax returns. Rates, thresholds and dates change. Confirm your own position with your registered tax or BAS agent.
Fifteen minutes on the phone is enough to tell you whether a dedicated bookkeeper suits your practice and what it would cost.
