How this usually works
A good medical accountant process starts with a short discovery to understand your practice model, locations, practitioner arrangements and software stack. That normally includes your PMS/EHR (for example Best Practice, MedicalDirector, Genie, Zedmed, Cliniko or Dental4Windows) and your accounting platform (Xero, MYOB or QuickBooks).
From there the work typically runs in three layers:
- Immediate triage: stabilise bank feeds, catch up coding, reconcile Medicare/MBS and private health remittances, fix payroll/STP issues and lodge any urgent BAS or IAS.
- Process design: document the daily cash-up, banking and remittance flow; set rules for GST-free vs taxable items; configure a chart of accounts for billings, receipts and service fees; implement fee-split statements and practitioner payouts.
- Ongoing review: deliver monthly management reports, keep BAS/payroll on time, monitor margins by practitioner or site, and map year-end tax planning well before deadlines.
If you already know you need help with medical bookkeeping, medical payroll or a medical tax accountant, use those targeted pages to go deeper.
Australian context to keep in view
- GST-free health supplies: many clinical services are GST-free when criteria are met, but some products and cosmetic/non-therapeutic items are taxable. Mixed supplies require sensible apportionment rules.
- MBS and insurer reconciliation: daily EFTPOS/Tyro/HICAPS banking should line up with Medicare, DVA and private health remittances. Variances and write-backs need clear handling.
- Service-entity models: practices often deduct a service fee and pay practitioners a split. Accurate statements, contractor records and tax treatment are essential.
- Payroll and awards: align rosters, penalty rates and allowances with relevant awards (for example Health Professionals and Support Services Award or Nurses Award), plus STP Phase 2 and super obligations.
- Privacy and data: ensure accounting workflows respect patient confidentiality and system access controls when connecting PMS to accounting software.
- State and federal obligations: watch for state-based payroll tax rules that may affect certain practice arrangements, plus federal BAS, PAYG, income tax and FBT settings.
What to compare before you commit
Scope
Confirm the scope covers bookkeeping, MBS/private health reconciliation, BAS/IAS, payroll, year-end tax and any advisory you need (pricing, cash flow, budgets or multi-site reporting).
Software fit
Ask about experience with your PMS/EHR (e.g. Best Practice, MedicalDirector, Genie, Zedmed, Cliniko, Dental4Windows) and your ledger (Xero/MYOB/QuickBooks). Look for workflow knowledge, not just software names.
Turnaround and communication
Agree on a monthly schedule for cash-ups, remittance reconciliation and management reports, plus how urgent items are escalated during busy clinics.
Commercial fit
Compare fixed fees vs hourly, what’s included, meeting rhythm, and practical reporting packs that clarify billings, receipts, service fees, wages and margins.
Best next steps
Write down the outcome you want: clean reconciliations, on-time BAS, reliable payroll, clearer management reporting, or support to restructure practitioner arrangements.
Collect a small pack for faster onboarding: last BAS, PMS end-of-day summaries, recent insurer/Medicare remittances, current fee schedules, payroll registers and your chart of accounts.
Then shortlist providers against that outcome. Use these pages to move into the most relevant subtopic, comparison or service hub before you make contact: medical bookkeeping, medical payroll, medical tax, plus broader hubs like Bookkeeping Services, Payroll Services, Tax Accountant and the Help Centre.
Frequently asked questions
Why do medical practices benefit from a specialist medical accountant?
Healthcare combines GST-free rules, MBS and insurer remittances, fee-split models and award-driven payroll. A specialist medical accountant is used to these patterns and the software that supports them, so you get cleaner books, clearer reporting and fewer surprises at BAS and year end.
Do doctors and medical practices charge GST?
Many services by registered health professionals are GST-free when criteria are met. However, some items (certain consumables, products or cosmetic/non-therapeutic services) can be taxable. If you have both, your books need clear coding and input tax credit apportionment. A medical accountant can set practical rules so this runs smoothly.
How should practitioner payments and fee splits be recorded?
Most clinics collect patient receipts, deduct a service fee and pay practitioners the balance. You’ll want reliable daily banking, MBS/private remittance reconciliation, itemised statements, correct contractor vs employee treatment and clear tax handling. Your accountant should design this flow so it’s repeatable and auditable.
What should I compare before choosing a provider?
Check scope, PMS/ledger experience, turnaround, reporting depth and communication style. Ask for a sample monthly pack that shows billings, receipts, service fees, wages, super and margins by site or practitioner. A short trial period can confirm fit.