Medical practices do not have a bookkeeping problem so much as a reconciliation problem. Money arrives from Medicare, from private health funds through HICAPS, from Tyro and from patients directly, usually net of fees and batched, while the record of what was actually billed sits in your practice-management software. Keep those two apart and your revenue, your fees and your tax are all estimates. We put them back together.

What medical practices actually need from a bookkeeper

  • Medicare and bulk-billing reconciliation, so a batched deposit is split back into real gross billings, the fees taken out, and what hit the bank.
  • Practitioner payments done correctly, whether doctors are employees or on service-fee arrangements, with STP and super handled.
  • GST treated properly, because most medical services are GST-free but some (cosmetic work, certain reports and medicals) are taxable, and getting the mix wrong flows straight into your BAS.
  • Your practice software mapped into Xero, so the clinic's billing data and the accounting match.
  • Reporting you can read, billings and margin by practitioner, not a single net number.

Medicare, bulk-billing and HICAPS reconciliation

This is the part most generic bookkeepers get wrong. Medicare Online and ECLIPSE deposits, Tyro settlements and HICAPS payments all arrive net and lumped together. We reconcile those payments against the claims and invoices in Cliniko, Gentu, Best Practice, Zedmed or Halaxy, so your books show the true gross billings, the fees deducted, and the net received, rather than matching a deposit to income and quietly losing the fees.

Practitioner payments and the payroll tax question

How you pay your doctors is the highest-stakes decision in a medical practice's books. Some are employees; many work under service-fee arrangements as contractors. In a number of recent cases, state revenue offices have treated those service-fee payments as wages for payroll tax, which has caught practices off guard. Whether your arrangement is affected depends on your specific contracts, how money actually flows, and which state you are in.

Our job is to record payroll and the money flow accurately so your position is clear and your STP and super are right. The assessment of your payroll tax exposure and how to structure arrangements is advice for your accountant or a specialist adviser, and we work alongside them rather than stepping into their lane. If you want to understand the issue first, read our guide to payroll tax on contractor GPs and medical practices.

GST-free versus taxable medical services

Most of what a medical practice bills is GST-free, but not all of it. Cosmetic procedures, some medico-legal reports, certain pre-employment and insurance medicals and other non-clinical services can be taxable. If the coding is wrong, it shows up as an incorrect BAS and either overpaid or underpaid GST. We make sure each revenue type is coded correctly so your BAS is right the first time.

Your practice software, into Xero

We keep the accounting in Xero and let your clinical system do what it does well. The work that matters is mapping the billing, payment and fee data from Cliniko, Gentu, Best Practice, Zedmed or Halaxy into Xero accurately, so there is one true set of numbers. Set that up properly once and reconciliation each month becomes a check, not a rebuild.

Fixed-fee, no lock-in

Bookkeeping from $300 per month, BAS from $150, and practitioner payroll from $20 per payslip, all fixed monthly fees. The exact number depends on your billing volume, how many practitioners you pay and how many systems need reconciling. You get a clear quote after a free call.

Running a medical practice and not sure your Medicare reconciliation or practitioner payroll is right? Book a free call and we will take a look. No obligation, no lock-in.