Can you run payroll for a medical practice?

Yes, within an agreed scope and payroll calendar. The practice remains responsible for providing complete approved pay data.

Can an exempt clinic recover VAT on costs?

Usually recovery is restricted for costs relating to exempt supplies; mixed activities may require partial-exemption calculations.

Which bookkeeping software should I use?

Choose software that matches your receipts, payroll and reporting needs. We can review the setup before agreeing the workflow.

Tax & practice services

Healthcare VAT, payroll and bookkeeping services

Connected bookkeeping, payroll and VAT support for medical practices, dental clinics and care providers. Agree what is handled, when and by whom.

Fixed fees, specialist healthcare accountants, and every HMRC and NHS Pensions deadline handled.

Fixed monthly fee — no surprises
Specialist in NHS pension and healthcare tax
Onboarding within 48 hours

Get my fixed-fee quote Book a free 15-min tax review

ICAEW & ACCA regulated
5,000+ clients served by ACCOTAX
Specialist healthcare accountants

Reviewed by Waqas Sagar ACA FCCA FMAAT · Last reviewed: 8 October 2026 · Updated for the 2026/27 tax year

Key takeaways

Your actual working arrangements determine the tax treatment; choosing a package does not change your employment status.
Keep records for each income source and check the official guidance linked to the questions below.
Agree the accounts, returns and advisory work you need before accepting a written fixed-fee quote.

Which accountancy support fits your income?

Start with how you are paid. Different income sources can need different accounts, returns and expense checks.

How you work	What we check	Support to explore
Employed or umbrella (PAYE)	Tax codes, eligible employment expenses and whether a tax return is needed.	Healthcare tax refund support
Genuinely self-employed	Business income and expenses, Self Assessment and MTD eligibility.	Healthcare Self Assessment service
Your own limited company	Company accounts, Corporation Tax, director income and off-payroll status where relevant.	Healthcare limited company accounts
Partnership	Practice accounts, allocated profit and each partner’s personal tax position.	Healthcare partnership accounts

Sound familiar?

Problems we fix for nurses, midwives and healthcare assistants

"I can't decide between umbrella, limited company or self-employed agency work."
"My bank shifts are on emergency tax."
"I've never claimed my NMC fees, uniform or mileage."
"I work for several employers and my tax codes are a mess."
"I do aesthetic work and don't know about VAT."

What it's costing you

Leaving it unfixed is rarely free

Overpaid tax: Unclaimed expenses and wrong tax codes mean paying more than you owe, year after year.
HMRC penalties and interest: Late returns attract automatic penalties, plus interest on tax paid late.
Lost evenings: Hours spent on forms, invoices and spreadsheets after a long shift.

General examples — your position depends on your own figures.

How we solve it

What we actually do for you

Refund claims

We check what you've overpaid and claim it back from HMRC.

Agency structure advice

A clear comparison of the ways you can be paid.

Self Assessment

Your return filed correctly, with every allowable expense.

Aesthetic VAT check

We confirm whether your treatments are exempt or standard-rated.

How we help

Healthcare VAT

Assess taxable, zero-rated and exempt supplies, registration and input-tax recovery.

Practice payroll

Process agreed pay data, RTI submissions and pension reporting with clear approval deadlines.

Cloud bookkeeping

Reconcile banks, patient receipts, supplier invoices and payment-provider charges.

Monthly reporting

Explain debtor balances, payroll costs and cash flow before annual accounts are due.

What to know before you decide

Exempt, zero-rated and standard-rated: why the distinction matters

Healthcare businesses can make more than one category of supply. Exemption can restrict input VAT recovery, while zero-rated sales are taxable at 0%. Review supplier status, treatment purpose and the contractual arrangement before coding a receipt. If you have mixed activities, partial exemption may apply to overheads; a clinic-wide assumption is rarely enough.

An agreed monthly process prevents year-end gaps

Set deadlines for bank access, purchase invoices, approved hours, starters and leavers. Decide who checks variable pay, patient refunds and supplier balances. The accountant’s role and the practice’s approvals should be written down, including what happens when records arrive late. Payroll, bookkeeping and VAT can be quoted together, but they are not automatically included in every package.

Your questions answered

Are my services exempt or standard-rated?

Medical care provided by registered health professionals is generally VAT exempt if the primary purpose is protecting health. Purely cosmetic procedures and medicolegal reports are typically standard-rated at the prevailing rate. You must monitor your taxable turnover against the £90,000 registration threshold. Determining the correct liability requires a detailed review of your specific services.

Check the official guidance · www.gov.uk Want us to check this for you? Get a free review →

What is partial exemption?

Partial exemption applies when a healthcare business makes both VAT-exempt and taxable supplies. You cannot usually reclaim all input VAT if you have exempt income. A specific calculation determines how much VAT on overheads is recoverable. This is a common requirement for GPs and consultants with mixed income streams.

Check the official guidance · www.gov.uk

Help with this question: VAT Registration & Returns for Doctors & Healthcare Professionals

Help with this question: Payroll & Pensions for Doctors & Healthcare Professionals

Want us to check this for you? Get a free review →

What happens if I registered late?

Failure to register for VAT when your taxable turnover exceeds £90,000 may result in financial penalties. HMRC may also charge interest on the VAT that should have been paid from the effective date of registration. You will be liable for the VAT on past sales regardless of whether you charged it. Early disclosure often helps in mitigating these penalties.

Want us to check this for you? Get a free review →

Quick quote

See what you could save — get a fixed fee in one working day

Three fields. No obligation. A specialist replies, not a sales team.

Packages for your working life

Accountancy packages for healthcare professionals

Self-employed income, a limited company, PAYE or a mixture: start with the support that matches how you actually work. We check your status and agree the scope and fee before starting.

Self-employed accountants for healthcare professionals packages

For genuine sole-trader income. We prepare your business accounts and Self Assessment, review allowable expenses and explain payments on account.

Sole-trader accounts and personal tax return
Allowable business expenses reviewed
Tax reserve and payment deadline guidance
MTD support scoped separately where required

Fixed fee quoted after a review

Discuss this package

Limited company accountants for healthcare professionals packages

For clinicians working through their own company. Choose Essential/Compliance, Core/Complete or Growth according to your accounts, bookkeeping and payroll needs.

Statutory accounts and Corporation Tax return
One director return for salary and dividends from the same company
Confirmation statement support; filing fee extra
Bookkeeping, VAT and payroll according to your chosen plan

Company packages from £45.83 + VAT / month

Compare company packages

Personal tax return packages for healthcare professionals

For employed clinicians, partners and people with mixed income who need a return. We check whether Self Assessment is required and reconcile the relevant income, expenses and pension tax information.

Self Assessment requirement checked
PAYE and other income reconciled
Eligible employment expenses reviewed
Pension tax work agreed separately where needed

Fixed fee quoted after a review

Discuss this package

Employment status is determined by the facts, not the package you choose. PAYE, umbrella and partnership arrangements may also apply. A limited company does not override IR35 or off-payroll rules, and not every employed clinician needs a tax return.

Overpaid tax?

Tax refund support for healthcare professionals

We review tax codes, eligible professional expenses and overpaid tax, then prepare a claim where you qualify. A refund is not guaranteed; HMRC decides the claim.

£249 + VAT

For refunds up to £5,000, our fee is £249 plus VAT. For refunds above £5,000, add 5% of only the amount above £5,000 to the £249 fee. VAT applies to the total professional fee.

Example: a £6,000 refund means £249 + £50 = £299 plus VAT.

Illustrative refund amount (£)

Professional fee, excluding VAT

£249

Ask about a tax refund

This illustrates the fee only, not whether you qualify or how much HMRC will refund. We agree the claim scope and payment terms before work starts.

What's included

Limited company packages — compare what's included

Essential/Compliance

For locums, salaried GPs and dentists with a limited company

from £45.83 + VAT /month

FRS 105 or FRS 102 1A statutory accounts
Corporation tax return (CT600) and tax computation
Confirmation statement preparation and filing support
One director Self Assessment return
Deadline reminders ahead of every filing date

Core/Complete

For private practice, consultants and associate dentists

from £62.50 + VAT /month

Everything in Essential/Compliance
Monthly bookkeeping and bank reconciliation
Quarterly Making Tax Digital VAT returns
Director payroll with RTI filing and pension submissions
Quarterly review call on numbers and tax position

Growth

For clinics, dental practices and growing medical teams

from £75.00 + VAT /month

Everything in Core/Complete
Payroll for up to five employees

Prices exclude VAT. Making Tax Digital quarterly updates available as an add-on. Compare fees

Why clinicians trust us

Chartered accountants who know the NHS

ACCOTAX has served over 5,000 clients.
Regulated chartered accountants (ICAEW and ACCA).
Founded by Waqas Sagar ACA FCCA FMAAT, with 18+ years' experience.

Reviewed by Waqas Sagar ACA FCCA FMAAT

Chartered accountant and founder of ACCOTAX. Last reviewed October 2026.

Get my fixed-fee quote

How it works

01
Free call
A 15-minute chat about your income, structure and deadlines.
02
Onboarding in 48 hours
We set up your records, software and HMRC agent access.
03
We handle the rest
HMRC, NHS Pensions and every deadline, with reminders before each one.

Free resource

Get the nurse expenses checklist free

Tell us where to send it and we'll email it to you.

Your questions, answered

Can you run payroll for a medical practice?: Yes, within an agreed scope and payroll calendar. The practice remains responsible for providing complete approved pay data.
Can an exempt clinic recover VAT on costs?: Usually recovery is restricted for costs relating to exempt supplies; mixed activities may require partial-exemption calculations.
Which bookkeeping software should I use?: Choose software that matches your receipts, payroll and reporting needs. We can review the setup before agreeing the workflow.

Speak to a specialist today

Leave your details and we'll call you back, or book a free review straight away.

Book a free 15-min tax review

Related healthcare expertise

VAT Registration & Returns for Doctors & Healthcare Professionals Payroll & Pensions for Doctors & Healthcare Professionals Accountants for aesthetic, cosmetic and skin clinics Accountants for opticians and optometry practices Accountants for pharmacists and independent pharmacies

Accountants for healthcare professionals Healthcare tax questions answered

General information for the 2026/27 tax year, prepared from the official guidance linked below. It is not personalised tax or regulated financial advice. Rules and circumstances can change; confirm your position before acting.

Official guidance

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