Medical.Accountants
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Payroll & Pensions for Private Clinics

Payroll & Pensions for private clinics. RTI errors? We fix it: fixed fees, ICAEW-regulated specialists. Free quote.

What does payroll & pensions for private clinics involve?

Our payroll & pensions service for private clinics covers payroll processing, rTI, payslips. It solves the problems we see most often — private clinics: RTI errors, auto-enrolment duties, NHS Pension deductions, minimum-wage compliance — on a fixed monthly fee agreed in writing before any work starts.

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

Reviewed by Waqas Sagar ACA FCCA FMAAT, Founder of ACCOTAX, 18+ years' experience · Last reviewed: 8 October 2026 · Updated for the 2026/27 tax year

Medical.Accountants by ACCOTAX, ICAEW/ACCA-regulated chartered accountants, London, serving clients across the UK. Over 5,000 clients served.

Key takeaways

  • Problems solved: Private clinics: RTI errors, auto-enrolment duties, NHS Pension deductions, minimum-wage compliance.
  • Included: Payroll processing.
  • Included: RTI.
  • Included: payslips.

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 workWhat we checkSupport to explore
Employed or umbrella (PAYE)Tax codes, eligible employment expenses and whether a tax return is needed.Healthcare tax refund support
Genuinely self-employedBusiness income and expenses, Self Assessment and MTD eligibility.Healthcare Self Assessment service
Your own limited companyCompany accounts, Corporation Tax, director income and off-payroll status where relevant.Healthcare limited company accounts
PartnershipPractice accounts, allocated profit and each partner’s personal tax position.Healthcare partnership accounts

Sound familiar?

Problems we fix for healthcare businesses

  • "I'm unsure which of our services are medical and which are cosmetic for VAT."
  • "Are our clinicians employees, contractors or inside IR35?"
  • "Fleet and equipment costs are eating our profit."
  • "Invoice finance is managing our cash flow, not us."
  • "We may qualify for R&D relief or SEIS/EIS."
  • "Investors want proper management accounts."

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

VAT and status review

VAT treatment and clinician status checked together.

Capital allowances

Relief claimed on vehicles and equipment.

R&D claims

Claims prepared where your work qualifies.

Management accounts

Monthly numbers investors and lenders trust.

How we help

01

Payroll processing

Part of our payroll & pensions service for private clinics, delivered on a fixed fee.

02

RTI

Part of our payroll & pensions service for private clinics, delivered on a fixed fee.

03

payslips

Part of our payroll & pensions service for private clinics, delivered on a fixed fee.

04

auto-enrolment

Part of our payroll & pensions service for private clinics, delivered on a fixed fee.

What to know before you decide

Your questions answered

What does a payroll service include?

Care staff must be paid at least the National Minimum Wage for all working time, including travel between visits. Averaging pay over a pay period is allowed but must be checked. A clear rota-to-payroll process and pension auto-enrolment checks keep costs predictable.

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

What is RTI?

Real Time Information (RTI) requires employers to report payroll data to HMRC on or before every payday. This process ensures tax and National Insurance calculations remain accurate throughout the year. You must submit a Full Payment Submission for each pay period. Our team manages these digital filings for medical practices to ensure compliance.

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

What are auto-enrolment pension duties?

Most NHS doctors and many healthcare staff are members of the NHS Pension Scheme. Contributions are deducted through payroll, and locum or private work can count only through the correct forms. High earners should check the annual allowance each year, as pension growth can trigger a tax charge.

Check the official guidance · www.gov.uk

Help with this question: NHS Pension Tax & Annual Allowance for Doctors & Healthcare Professionals

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How are NHS Pension deductions handled in payroll?

Care staff must be paid at least the National Minimum Wage for all working time, including travel between visits. Averaging pay over a pay period is allowed but must be checked. A clear rota-to-payroll process and pension auto-enrolment checks keep costs predictable.

Check the official guidance · www.gov.uk

Help with this question: NHS Pension Tax & Annual Allowance for Doctors & Healthcare Professionals

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

What is the National Minimum Wage rule for my staff?

Employers must pay staff at least the statutory minimum rate based on their age and apprenticeship status. These rates typically increase every April. You must maintain accurate records of hours worked to prove compliance. Failure to pay the correct rate can result in significant penalties and public naming by the government.

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

How much does outsourced payroll cost?

Our packages for private clinics start at £45.83 + VAT a month, with Core at £62.50 and Growth at £75 + VAT. The right package depends on your income sources, whether you trade through a company and any payroll, VAT or pension work. We confirm the exact fee in writing before any work begins, so there are no surprise invoices.

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

What year-end forms do employers send?

Employers must submit a final payroll report and provide employees with a P60 by 31 May. You may also need to file P11D forms for taxable benefits by 6 July. These documents summarise total pay and deductions for the tax year. Medical.Accountants handles these filings as part of our payroll service.

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

Can you take over payroll mid-year?

Care staff must be paid at least the National Minimum Wage for all working time, including travel between visits. Averaging pay over a pay period is allowed but must be checked. A clear rota-to-payroll process and pension auto-enrolment checks keep costs predictable.

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

Are medical services VAT exempt in the UK?

Most health care by registered professionals is VAT exempt where the main purpose is protecting or restoring health, so many clinicians never register. VAT becomes relevant when you sell goods, provide cosmetic or medicolegal services, or exceed the registration threshold with taxable income. HMRC Notice 701/57 gives the official guidance.

Check the official guidance · www.gov.uk

Help with this question: VAT Registration & Returns for Private Clinics

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

When must a healthcare business register for VAT?

Welfare services such as residential and domiciliary care are VAT exempt when supplied by a provider regulated by the relevant state regulator, such as CQC in England or Ofsted for children's homes. Unregulated elements, introductory agency fees and some supported living services can be standard-rated. HMRC Notice 701/2 explains the conditions.

Check the official guidance · www.gov.uk

Help with this question: VAT Registration & Returns for Private Clinics

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

Which healthcare services are standard-rated for VAT?

Welfare services such as residential and domiciliary care are VAT exempt when supplied by a provider regulated by the relevant state regulator, such as CQC in England or Ofsted for children's homes. Unregulated elements, introductory agency fees and some supported living services can be standard-rated. HMRC Notice 701/2 explains the conditions.

Check the official guidance · www.gov.uk

Help with this question: VAT Registration & Returns for Private Clinics

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

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.ukWant 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 Private Clinics

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.

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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 practice owners

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 practice owners 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 practice owners 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 practice owners

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 practice owners

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.

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

  1. 01

    Free call

    A 15-minute chat about your income, structure and deadlines.

  2. 02

    Onboarding in 48 hours

    We set up your records, software and HMRC agent access.

  3. 03

    We handle the rest

    HMRC, NHS Pensions and every deadline, with reminders before each one.

Free resource

Get the healthcare business finance checklist free

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

Your questions, answered

Do private clinics need payroll & pensions?
Most health care by registered professionals is VAT exempt where the main purpose is protecting or restoring health, so many clinicians never register. VAT becomes relevant when you sell goods, provide cosmetic or medicolegal services, or exceed the registration threshold with taxable income. HMRC Notice 701/57 gives the official guidance.
What does payroll & pensions for private clinics include?
Most health care by registered professionals is VAT exempt where the main purpose is protecting or restoring health, so many clinicians never register. VAT becomes relevant when you sell goods, provide cosmetic or medicolegal services, or exceed the registration threshold with taxable income. HMRC Notice 701/57 gives the official guidance.
How much does it cost for private clinics?
Our packages for private clinics start at £45.83 + VAT a month, with Core at £62.50 and Growth at £75 + VAT. The right package depends on your income sources, whether you trade through a company and any payroll, VAT or pension work. We confirm the exact fee in writing before any work begins, so there are no surprise invoices.
What are the deadlines for private clinics?
Most health care by registered professionals is VAT exempt where the main purpose is protecting or restoring health, so many clinicians never register. VAT becomes relevant when you sell goods, provide cosmetic or medicolegal services, or exceed the registration threshold with taxable income. HMRC Notice 701/57 gives the official guidance.
Can I switch to you mid-year?
Switching takes minutes on your side. You sign our engagement letter, we contact your previous accountant for professional clearance and records, and we take over HMRC and Companies House authorisations. You can switch mid-year; we pick up from the last filed return.

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

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 sources referred to on this page: HMRC VAT Notice 701/57; HMRC Notice 706 partial exemption; HMRC VAT registration (GOV.UK); HMRC MTD for VAT.

Official guidance

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