An affordable bookkeeping service for physiotherapy practices in Melbourne
A physiotherapy practice running private health, WorkCover, NDIS and direct billing simultaneously is managing four income streams that each need to be recorded completely differently
Bookkeeping for physiotherapy practices
Do any of these financial scenarios sound familiar as a physiotherapist?
- Private health fund rebates and patient gap payments are not reconciling cleanly against your practice billing system and you have never pinpointed why.
- Your NDIS clients are billed through the portal but you are not certain the income is being recorded at the right time or with the right treatment in your accounting software.
- WorkCover claims have an approval cycle that makes income recognition confusing and you are not sure what is recorded versus what is still outstanding.
- You run Pilates or gym-based rehabilitation programs alongside clinical physiotherapy and you are not certain whether those services are GST-free or taxable.
- Associate physiotherapists or exercise physiologists on your team have never had their arrangement formally assessed for employment versus contractor classification.
- Your Health Professionals Award payroll rates for physio assistants and reception staff have not been reviewed since they were first set up
If any of these sound like your practice, you are not alone and there is a straightforward fix.
A bookkeeper in Melbourne for physiotherapy practices
A physiotherapy practice has one of the most complex income profiles of any allied health business in Australia.
- Private health fund rebates through HICAPS arrive separately from the gap payment collected at the time of the appointment, and both must be reconciled against what the billing system recorded for each session.
- WorkCover income involves an approval process before payment is authorised, a claim submission that differs from standard health billing, and a payment timeline that does not align with when the service was delivered.
- NDIS income depends on the participant’s plan management type, with agency-managed clients billed directly to the NDIA, plan-managed clients invoiced to a plan manager, and self-managed clients invoiced directly, each with different approval and payment timelines.
- Direct private paying patients are the most straightforward but still must be reconciled against the billing system to ensure no session goes unrecorded or unrecovered.
When all of these income streams are being recorded from bank deposits rather than from the billing system, the income figure in the accounting software reflects the timing of payments rather than when the clinical work was done.
This produces a profit and loss statement that varies with payment cycles rather than with actual activity, a GST position that is difficult to verify, and a BAS that cannot be prepared with confidence because the revenue figure cannot be reconciled to the clinical records.
The GST treatment of physiotherapy services adds further complexity specific to this profession. Core physiotherapy consultations are GST-free as health services. Clinical Pilates delivered as a one-on-one therapeutic program by a physiotherapist may also be GST-free.
However, group Pilates classes, gym memberships, and exercise programs that are not provided in the context of an individual therapeutic treatment plan are likely taxable.
Practices that run studio programs alongside clinical services are operating a mixed-supply business and must apply different GST treatment to different revenue streams or the BAS will be incorrect by design.
What a bookkeeper can manage for a physiotherapy practice in Melbourne
A physiotherapits practice has financial flows that are different to many other business types, so managing them correctly requires understanding and needs to cover these activities;
- Billing system reconciliation.
Every private health fund, HICAPS, WorkCover, DVA, NDIS and direct patient payment is reconciled against the billing system so that income in the accounting software reflects actual service delivery rather than payment timing. Income that has been billed but not yet received is tracked through the accounts receivable position.
- NDIS income recording.
Income is recorded with the correct treatment for each participant’s plan management type and reconciled against NDIS portal claims. The timing of income recognition reflects when services were delivered and claims were submitted rather than when the NDIA processed the payment.
- GST treatment across clinical and non-clinical services.
Therapeutic physiotherapy services are correctly coded as GST-free. Non-therapeutic programs, group fitness classes and gym memberships are correctly coded as taxable. The BAS reflects the actual mixed-supply position of the practice.
- Associate physiotherapist and exercise physiologist arrangements.
Each associate or contractor arrangement is assessed against the ATO’s employment test. Super and PAYG withholding obligations are calculated and applied where required. The practice is not carrying an undisclosed super liability for arrangements that have never been formally assessed.
- Health Professionals and Support Services Award payroll.
Physiotherapy assistants, exercise physiologists and reception staff are paid at the correct classification level under the current award rates, reviewed annually after each Fair Work wage review. STP lodged every payday. Payslips issued on time.
- BAS preparation and lodgment.
Prepared from fully reconciled records with the correct mixed-supply GST treatment applied. Lodged by a registered BAS agent with the four-week extension on both lodgment and payment.
- Profit and loss reporting.
Revenue reported by income stream so the practice owner can see the relative contribution of private health, NDIS, WorkCover and direct billing to overall practice performance.
A certified and qualified bookkeeper
Working with Clients Needs Bookkeeping means the financial administration of your practice is handled end to end by a registered BAS Agent who understands the specific requirements of a dental business. In practical terms, this covers:
Why a registered BAS agent is non-negotiable for an allied health practice
Only a registered BAS agent is legally authorised to prepare and lodge your BAS and advise on your GST position. Registration also provides safe harbour protection against penalties arising from errors the agent makes. The automatic four-week lodgment and payment extension applies to every quarterly BAS lodged through a registered agent. Matthew Powell is registered with the Tax Practitioners Board. Verify at tpb.gov.au.
Software credentials: MYOB Diamond Partner, MYOB Certified Consultant, Xero Silver Champion Partner, Xero Advisor Certified, Xero L2 Certified Professional, Xero Payroll Specialist. Also works with QuickBooks and other platforms.
About Matthew Powell, registered BAS agent and bookkeeper
Matthew Powell is the director of Clients Needs Bookkeeping and a registered BAS Agent with more than 15 years of experience working with small and medium businesses across Melbourne and the Mornington Peninsula.
He works across MYOB, Xero, and QuickBooks, and has particular depth of experience in health and medical practice bookkeeping, including dental, medical, and allied health clients.
Matthew is known for being accessible, clients regularly comment that he responds quickly, handles problems promptly, and communicates in plain language rather than accounting jargon.
He works with business owners from any industry sector or niche who provide services or sells products. He does your bookkeeping remotely and takes on new clients with the intent of building a long-term relationship rather than processing a transaction.
Bookkeeping Packages start from $150 per month. The first consultation is free.
Read some of our bookkeeping case studies
Below are real life examples from businesses like yours who needed to use a bookkeeper.
Frequently asked questions before hiring a bookkeeper
Is clinical Pilates GST-free?
Clinical Pilates delivered as a one-on-one therapeutic program by a registered physiotherapist in the context of an individual treatment plan is generally GST-free as a health service. Group classes and studio programs that are not part of an individual therapeutic treatment are generally taxable. The distinction matters for the BAS and must be applied consistently at the transaction level.
How does NDIS income get recorded correctly?
NDIS income recognition depends on the participant’s plan management type. Agency-managed claims are lodged through the NDIS portal and income is recognised when the claim is approved and paid. Plan-managed clients are invoiced to the plan manager and income is recognised on the invoice. Self-managed clients are invoiced directly. Matthew records each type correctly and reconciles the accounting file against portal claims and payment receipts.
Our associates invoice us monthly for a percentage of their billings. Do we owe them super?
Possibly. The ATO assesses this based on the substance of the working arrangement rather than the structure of the invoicing. Associates who operate exclusively from your practice using your systems and patient base carry a significant risk of being assessed as employees for super purposes. Matthew assesses each arrangement on its specific terms.
What does bookkeeping cost for a physiotherapy practice?
Packages start from $150 per month. A solo physiotherapist with a simple setup has different requirements from a multi-disciplinary clinic with associates, a Pilates studio and a full NDIS caseload. The first consultation is free.
Ready to get the financial side of your chiropractor practice managed by a bookkeeper?
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You already know there are things in the books that are not right.
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The personal expenses that went through the business account during a tight month are still sitting there.
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The BAS is lodged but you are not entirely sure the figures are accurate.
None of these are unusual, and none of them are unfixable but every month they sit unresolved is another month of compounding risk.
Packages from
$150 per month
Structured around what your business actually needs
Registered & certified bookkeeper
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