Finding the right GP accountant services changes how you manage your medical practice finances. Whether you are a GP partner with a profit share to allocate, a salaried GP with locum income on the side, or a consultant building private work, a specialist medical accountant understands the structures and rules that general practitioners and hospital doctors actually face.

Unlike a high-street accountant, a medical specialist knows GMS and PMS contracts, the Global Sum and Carr-Hill weighting, QOF, the NHS Pension Scheme and the GP pension certificates. This guide is the hub: it walks through the full service range and links to the detailed guide for each area, so you can see what a complete medical accounting service looks like before you go deeper.

What GP Accountant Services Include

Professional GP accountant services go well beyond bookkeeping. A complete service for a UK practice or doctor usually spans:

  • Partnership accounts and the SA800, with profit allocation and capital account management for GP partnerships.
  • Personal self-assessment, covering partnership profit shares, salaried income, locum work and any private or media income.
  • NHS pension certification and planning, including the Type 1, Type 2 and locum forms and annual allowance work.
  • Payroll and PAYE for the practice team and salaried GPs.
  • VAT where private, cosmetic or medico-legal work brings it into scope.
  • Tax planning and incorporation advice for private work, weighed against the NHS pension consequences.
  • Bookkeeping, software and Making Tax Digital support to keep records compliant and quarterly updates on track.

The sections below introduce each area. For the underlying detail, follow the linked guide rather than expecting every number here, this page is the map, not the territory.

Partnership Accounts and Profit Sharing

GP partnerships have their own accounting rhythm. The partnership files an SA800 and each partner's profit share flows to the partnership pages of their personal return, taxed as trading income. A partner is taxed on their profit share, not their drawings, so getting the allocation right matters for every partner's tax position and NHS pension.

Profit shares can reflect seniority, sessions, list responsibilities and non-clinical roles, and the accounts also handle capital accounts on partner entry and exit, premises and equipment. We cover the mechanics in the GP partnership tax guide and the allocation choices in GP partnership profit sharing and tax planning. Where the practice income itself needs explaining, see how GMS funding works (Global Sum and Carr-Hill).

NHS Pension: Certificates and Annual Allowance

The NHS pension is the single most medical-specific part of the work, and it has two halves: getting the right certificate filed, and managing the annual allowance.

Certificates follow your role. A GP partner (Type 1) completes the Annual Certificate of Pensionable Profits; a salaried GP (Type 2) completes the Type 2 self-assessment; a freelance locum pensions income via Locum forms A and B through PCSE. We explain the locum route in NHS pension for locums (Form A and Form B).

On the tax side, the standard pension annual allowance is £60,000. It tapers where threshold income exceeds £200,000 and adjusted income exceeds £260,000, down to a floor of £10,000, and for a defined-benefit scheme the measure is the pension input amount (capitalised growth), not contributions paid. Note this is the level since April 2023, when the allowance rose from its former £40,000 and the floor rose from £4,000. The lifetime allowance was abolished from 6 April 2024 and replaced by the Lump Sum Allowance (£268,275) and the Lump Sum and Death Benefit Allowance (£1,073,100). Where a charge arises, Scheme Pays can settle it. The full detail sits in the NHS pension annual allowance guide and the Scheme Pays deadlines guide.

Personal Tax and Self-Assessment

Most doctors have more than one income source, which is where careful self-assessment earns its keep:

  • Partnership profit shares from NHS and private work.
  • Locum income from several engagements.
  • Teaching, training and appraisal fees.
  • Medical writing, media and consultancy work.
  • Investment income and let property.

A specialist accountant claims the right allowable expenses (the GMC retention fee, indemnity for private and non-clinical work, relevant Royal College and BMA subscriptions, and business mileage at the HMRC rate of 55p per mile for the first 10,000 business miles in 2026/27, 25p thereafter), applies Class 4 National Insurance at 6% then 2% (Class 2 is no longer a required payment), and handles HMRC correspondence. The full deductions checklist is in our GP tax deductions list for 2026, with the process covered in the GP tax return guide and broader strategy in GP tax advice.

Payroll, PAYE and the Practice Team

A GP practice is an employer. Salaried GPs, nurses, reception and admin staff all run through PAYE, with employer (secondary Class 1) National Insurance at 15% above the £5,000 secondary threshold and auto-enrolment pension duties. A specialist payroll service also handles the NHS pension employer side and starters and leavers cleanly. See GP payroll services for how this works in practice.

VAT for Medical Practices

Genuine medical care by a registered practitioner is exempt from VAT where the principal purpose is the protection, maintenance or restoration of health, and NHS GMS and PMS income is outside the scope of VAT. The watch-items are purely cosmetic or aesthetic work, medico-legal and expert-witness reports, and some occupational-health and administrative services, which can be standard-rated.

The VAT registration threshold is £90,000 of taxable (non-exempt) turnover (from 1 April 2024), with deregistration at £88,000, and only non-exempt turnover counts. A practice with both exempt and taxable supplies runs partial exemption. The detail, including when a doctor crosses the line, is in GP VAT registration.

Locum Doctors and IR35

Locum work has its own service strand. A freelance locum is usually a sole trader, but some operate through a personal service company, which brings the off-payroll (IR35) rules into play. For NHS Trust work the status determination sits with the Trust or fee-payer, not the locum; for medium and large private hirers it sits with the hirer; only small private clients leave the decision with the company. The off-payroll rules have not been abolished. We cover the engagement-by-engagement reality in the locum doctor tax guide and locum doctor IR35.

Incorporation and Private Practice

Incorporation is the area where specialist judgement matters most, because the headline tax comparison is only half the story. A limited company cannot hold an NHS GMS or PMS contract, and company income and dividends are not NHS-pensionable, so incorporation is a private-work decision and any tax saving has to be set against the loss of NHS pension accrual.

The tax machinery still moves with the year: corporation tax runs from 19% on profits up to £50,000 to 25% above £250,000 with marginal relief between, and dividend rates rose to 10.75% ordinary and 35.75% upper from 6 April 2026 (additional rate unchanged at 39.35%, allowance £500), which narrows the saving further. We model both sides in the medical practice incorporation guide, with the company tax detail in GP corporation tax and the mixed-income picture in private practice tax (NHS and private income).

Want this checked against your specific situation?

Leave your details and a one-line summary. A specialist medical accountant will reply within 24 hours, with no obligation.

Practice Sale, Goodwill and CGT

A point that surprises doctors moving from other sectors: NHS GP goodwill cannot be sold, and has not been saleable since 1 April 2004 (the current instrument is SI 2019/251). A GP transaction is about tangible assets, premises and capital accounts, not NHS goodwill. The only goodwill a GP can sell is private goodwill.

Business Asset Disposal Relief therefore applies only to a private-practice disposal or a share sale of an incorporated private practice. The BADR rate is 18% for a disposal on or after 6 April 2026 (it was 14% from 6 April 2025 to 5 April 2026, and 10% before that), within the £1m lifetime limit. The rules are set out in can GP practice goodwill be sold and selling a private medical practice (CGT and BADR).

Bookkeeping, Software and Making Tax Digital

Good records underpin every other service. Cloud bookkeeping gives a real-time view of the practice or your personal position and feeds into Making Tax Digital for Income Tax, which began for sole traders and landlords with qualifying income over £50,000 from 6 April 2026 (then £30,000 from April 2027 and £20,000 from April 2028). Limited companies are out, and general partnerships are deferred, but most full-time locums and unincorporated private GPs are in scope. See the GP bookkeeping guide for setting this up.

Choosing the Right Medical Accountant

Not every accountant understands medical practice. When comparing GP accountant services, look for:

  • Medical specialisation, a genuine focus on doctors and practices rather than a general client base.
  • NHS pension fluency, current on the annual allowance, the taper, Scheme Pays and the Type 1, Type 2 and locum certificates.
  • Contract knowledge, GMS, PMS, Global Sum, Carr-Hill, QOF and PCN income, not UDAs or dental concepts.
  • Regulatory awareness, the GMC, the NHS England Performers List and CQC, and which fees are deductible.
  • Modern systems, cloud software and a portal so records and updates stay current through the year.
  • Proactive advice, strategic planning around the annual allowance and incorporation, not just year-end compliance.

When to Engage Professional Help

Some situations make specialist GP accountant services worthwhile rather than optional:

  • Joining or leaving a GP partnership, or a buy-in or buy-out of capital.
  • Starting private practice alongside NHS work.
  • Considering incorporation of private work or restructuring.
  • Facing NHS pension annual allowance charges or a Scheme Pays decision.
  • An HMRC enquiry or a compliance question.
  • Planning retirement, partial retirement or succession.

Early engagement usually means better outcomes and less stress. If you want a sense of what a full service involves before committing, the breakdown in our guide to GP accountant cost sets out what is typically included at each level.

Getting Started

A specialist medical accounting relationship starts with understanding your situation, your role, your income mix and your pension position. Come prepared with recent accounts, your last tax return and any specific questions about your structure or NHS pension, and you will get tailored advice from the first conversation.

If you would like to talk it through, get in touch and we will explain how the service fits your practice or career stage.

This guide is general information, not personal tax advice. Medical Accountants UK specialises in accounting for GPs, practices and consultants, and figures are stated for the 2026/27 tax year unless otherwise dated.