How A Medical Accountant Can Help Your Business

As a doctor, you work long hours. You help people. You keep your community healthy. But when tax season hits, many doctors get stressed out and overwhelmed. 

Between PAYG income, private billings, ABN income, and practice expenses, your financial world isn’t simple. And yet, most doctors still use regular accountants — the same ones handling tradies, cafés, and salaried employees.

The result? Missed deductions. Incorrect business structures. And overpaid tax.

A specialist medical accountant understands how the medical industry works.

They know what tax deductions you can claim as a doctor, what the ATO is watching, and how to keep more of what you earn — all while keeping you compliant.

It’s not about “creative accounting”. It’s about having a smart, proactive tax strategy for your profession.

If you’ve ever wondered why your tax bill feels high even though you “don’t spend much”? It’s probably because your accountant isn’t looking at the full picture — your business structure, income sources, and timing of expenses.

That’s where a medical accountant can help.

Do You Need A Medical Accountant?

As a doctor, you’re classified as a high income earner and you’re probably paying a substantial amount in tax. You’re a specialist in your field who faces much more risk than the average employee.

You might work across multiple medical clinics. You likely bill private patients, receive Medicare payments, or run a medical practice through a company or trust.

Every one of those income streams is taxed slightly differently.

A general accountant can miss things, which leaves you open to legal and financial risk.

But a specialist medical accountant sees opportunities to split income, defer tax, maximise super contributions, or restructure your business setup for long-term savings.

Here’s how a medical accountant can help:

1. Managing multiple income streams

Doctors often mix PAYG and self-employed income. Without the right setup, you can end up paying more tax than you need to.

A medical accountant helps you choose the best structure (i.e. a company, trust, or partnership) to protect your assets and reduce your risk exposure. 

Understanding medical-specific rules.

Not everything you buy or bill is treated the same under tax law.

For example, some health services are GST-free under Medicare, while others (like cosmetic treatments) aren’t.

A specialist accountant knows these nuances and how to handle them correctly.

3. Purchasing new equipment

Buying new medical equipment or technology at the right time can have a huge impact on your tax position. 

A medical accountant helps plan major purchases strategically, so you maximise depreciation benefits and claim deductions in the right financial year.

4. Personal asset protection.

Many doctors have significant personal assets — homes, investments, and super. A good medical accountant helps structure your income so you’re protected if anything goes wrong (like legal disputes or practice liabilities).

5. Tax planning benefits.

If you only hear from your accountant at tax time, you’re missing out.

A medical accountant checks in with you throughout the year, assists with tax planning, helps with your practice management software, and keeps an eye on your cash flow.

In short: you don’t just need an accountant who can do your taxes.

You need a medical accountant who understands how your industry, your income, and your business actually works.

Tax Deductions For Doctors: What Can You Claim?

Here’s where most doctors leave money on the table.

Many doctors assume they can only claim the basics like uniforms, registration, and maybe a laptop. But the ATO allows a wide range of deductions for doctors and medical professionals, provided they’re legitimate business expenses used to generate income.

A good medical accountant knows how to identify every dollar you’re entitled to claim and how to document it properly.

Here are some of the tax deductions available to doctors:

Work-Related Expenses

• Professional registrations: AHPRA, specialist college memberships, and union fees.
• Uniforms and laundry: If they’re required, are a form of PPE, or have your clinic or practice logo embroidered.
• Education and training: CPD courses, conferences, workshops, and subscriptions to medical journals.
• Insurance: Professional indemnity, income protection, and business insurance.

Every dollar here adds up, and many doctors don’t realise how much of it can be claimed until a medical accountant reviews their records.

Home Office Costs

If you consult with patients online, prepare reports, or handle admin from home, part of your household expenses may be deductible if you have a dedicated office. This may include:

• Internet and phone costs (apportioned for work usage)
• Computer equipment and office furniture depreciation
• Electricity, rent, and running costs

If you don’t have a dedicated office, you can claim a fixed rate based on the number of hours you work each year.

Car and Travel Expenses

If you’re away from home overnight while working (e.g. interstate or overseas), you may be able to claim related travel expenses. This also applies if you travel between hospitals, clinics, or nursing homes during your work day.

Travel deductions include:

• Car expenses (using the logbook or cents-per-kilometre method)
• Parking and tolls
• Flights, food, and accommodation for locum work or conferences

The ATO’s travel rules are strict — so documentation is important.

A medical accountant can help you claim the maximum legal amount while still being compliant with the ATO.

Equipment and Technology

A medical accountant can help you deduct the cost of equipment and related technology that you use in your work, including:

• Laptops, tablets, diagnostic tools, stethoscopes, and medical instruments
• Practice software subscriptions
• Medical equipment depreciation

With the right planning, large purchases can be written off immediately (under current ATO instant asset write-off rules) or depreciated over time, depending on your setup.

Super Contributions

Doctors often earn a lot, but don’t always plan ahead for retirement savings.

By making personal deductible super contributions, you can lower your taxable income and build your future nest egg.

A medical accountant will calculate the optimal superannuation amount so you don’t exceed contribution caps and pay extra tax.

Professional Development

Medical learning never stops — and the ATO knows that.

Courses, workshops, and medical conferences (including travel if directly related) are usually all claimable, provided they relate to your current practice or specialisation.

Tax Deductions For Doctors: Here’s The Catch.

Claiming tax deductions is only part of the story.

If your accountant doesn’t understand how your business works, or how your income flows between entities, you could still be paying more tax than necessary.

For example:

A Perth GP operating as a sole trader or employee may benefit from incorporating as a company once their income passes a certain threshold. This allows them to access company tax rates, retain profits, and protect their personal assets.

The Benefits of a Medical Accountant

Medical accountants don’t just focus on tax. They help you take control of your financial health, the same way you help your patients take control of their physical health.

Here’s what that looks like in practice.

1. Year-Round Tax Planning

You shouldn’t be hearing from your accountant once a year.

A proactive medical accountant monitors your income and expenses throughout the year — spotting tax-saving opportunities early, not when it’s too late.

They’ll flag when to buy equipment, prepay business expenses, or contribute to super. It’s about planning ahead, not reacting to circumstances.

2. Smarter Business Structures

Are you still trading as a sole trader? Do you work as a medical employee? You could be paying more tax than necessary and exposing your personal assets.

A medical accountant can:

• Set up a company or trust to distribute income tax-effectively.
• Help protect you from professional risk or litigation.
• Make sure you’re compliant with ATO and Medicare rules.

The right business structure can save you thousands each year while giving you long-term flexibility.

3. Better Cash Flow Management

Between practice costs, staff, and equipment, money moves fast.

A medical accountant helps you:

• Forecast your income and expenses
• Track slow months
• Avoid cash flow issues or surprises

This is especially useful if you run a private practice where patient billings, Medicare, and private health payments can be delayed or get incorrectly coded.

4. Clarity and Confidence

You shouldn’t have to guess how your business is performing.

A medical accountant explains your numbers in plain English — without the tax jargon.

They’ll help you understand:

• Which services or procedures are bringing in the most profit
• Where your costs are creeping up
• How to reach your next financial target or business goals

When you understand your numbers and financial data, you make better decisions.

Choosing the Right Accountant

Choosing an accountant is like choosing a medical specialist — you want someone who understands your field.

Here’s what to look for when hiring a medical accountant:

Industry experience.

Ask how many medical clients they work with. A doctor’s financial setup and reporting is different from a plumber’s or a restaurant owner’s.

Clear communication.

Do they explain things simply? Do they reply quickly? If not, keep looking.

Proactive mindset.

Do they contact you before June? Do they suggest improvements or just lodge your tax return and BAS?

Integrated services.

Does your accountant offer bookkeeping, BAS, payroll, and virtual CFO services under one roof? 

Transparent fees.

Make sure there are no hidden extras. No surprise invoices. Just clear pricing with clear value. Either on an hourly rate or a fixed fee basis.

Team Culture

Do you like your accountant as a person? Are they honest, reliable, and respectful? Are they always learning and upskilling? Do they love what they do?

If they tick those boxes, you’ve found your person.

Accounting For Doctors: Common Mistakes

Even the smartest health professionals get caught out by tax traps. Here are the big ones we see every year:

1. Mixing business and personal expenses.

Do you mix business and personal expenses? Not only does it create more work for your bookkeeper, but you run the risk of claiming the wrong business expenses. If you can, try and keep your business and personal expenses separate.

2. Not reviewing your business structure.

Your business setup from five years ago might not suit your current income or growth. As your career or business evolves, your tax plan should too.

3. Missing BAS and super deadlines.

Busy schedules can lead to missed payments and ATO penalties. A medical accountant can automate these so you never fall behind.

4. Buying at the wrong time.

Purchasing new medical equipment in July instead of June could cost you a year of depreciation. Timing matters when it comes to tax.

5. Relying on a once-a-year accountant.

If your accountant only shows up for your tax return, you’re missing out on cash flow and growth opportunities during the rest of the year.

FAQs – Accountants for Doctors

1. Do doctors really need a specialist medical accountant?

Yes. Doctors often have complex income streams — a mix of salary, ABN, and practice income. A medical accountant ensures it’s structured and taxed correctly.

2. Can I claim my medical equipment and software?

Absolutely. Tools, software, travel, and equipment are usually deductible, provided they’re documented and relate to your employment or business income.

3. Is my professional development deductible?

Yes, as long as the training relates to your current practice or specialty. Conferences, workshops, and medical research journals all qualify.

4. I’m a GP working across multiple clinics. Do I pay tax twice?

No. Your income is combined for tax purposes — but the structure you use (company, trust, or sole trader) determines how it’s taxed and what deductions apply.

5. Can a medical accountant help with cash flow?

Yes. They can forecast your earnings, plan for slower periods, and help you manage BAS, super, and expenses so you always have enough cash on hand.

6. I’m starting a private practice. When should I get an accountant involved?

Before you open the doors. The setup stage is where the biggest tax savings happen — especially with your business structure, GST setup, and equipment purchases.

7. Can you work with my existing bookkeeper or software?

Yes. Most medical accountants work seamlessly with Xero, MYOB, and existing staff or admin teams. The goal is to simplify your financial setup.

8. Where is your firm based?

We’re based in Perth, but we work with businesses and doctors all over Australia. You can find us on Google here.

Ready To Hire A Medical Accountant?

You work hard to look after people — but when it comes to your own finances, it can feel like there’s no time to think about it.

Maybe you want to understand where your money actually goes. Maybe you’d like to save more, plan ahead, or just stop worrying about tax time.

You don’t need another accountant who only shows up once a year. You need someone who helps you plan, grow, and protect your income — all year round. When your finances are healthy, you have more time and headspace for what really matters: your patients, your practice, and your life outside work.

Contact us today to find out more.

Let’s make your finances and tax situation as healthy as possible.