GP practice accountants for partnerships and their partners
A GP practice is two jobs of accounting stacked on top of each other. There is the partnership itself, whose income arrives as global sum weighted by Carr-Hill, QOF achievement, enhanced services, PCN and DES payments and reimbursements, and whose accounts have to carry notional rent, capital and current accounts and a profit allocation that changes whenever a partner joins or leaves. Then there is each partner individually, with a profit share, superannuation already deducted at source, and often locum, out-of-hours or private income alongside it. Accountants for GP practices have to make both sets of figures agree, which is where generalist practice accounting most often comes apart.
Note: Statutory figures for the tax year shown. Your own position is what decides the answer.
What we hear
What we hear from GP practices, partners and salaried GPs
The questions and concerns that come up most in the first conversation.
Does our practice income reconcile to what PCSE says it paid us?
Practice income does not arrive as one figure. Global sum is weighted by the Carr-Hill formula for the age and sex, additional needs, list turnover, care home, rurality and staff cost profile of your list. QOF is paid partly in aspiration and settled on achievement. Enhanced services, PCN and DES payments, and reimbursements for premises, drugs and locum cover all land separately, some in arrears. The reconciliation between the PCSE statements and the practice ledger is where accountants for GP practices earn their keep, because a payment that was never chased is invisible in accounts that simply record what arrived.
How should notional rent and the capital accounts be handled?
Notional rent is reimbursement for premises the partnership occupies, and how it is treated depends on who owns the building and on what terms. Sitting alongside it, each partner has a capital account (their stake in the practice assets) and a current account (undrawn profit). Confusing the two is the commonest defect in GP practice accounts prepared by generalists, and it matters most at exactly the moment a partner joins, retires or asks what their share is actually worth.
Am I facing an NHS pension annual allowance charge?
The NHS Pension Scheme is defined benefit, so your pension input amount grows with pensionable pay even if you pay in nothing extra. The annual allowance is £60,000 for 2026/27, unchanged from 2025/26, and it tapers by £1 for every £2 of adjusted income above £260,000 where threshold income also exceeds £200,000, down to a floor of £10,000. Because the measure is capitalised growth rather than contributions paid, a good year for the practice can produce a charge with no warning. Pension input, threshold income and adjusted income are modelled annually, and carry-forward from the three previous tax years is checked before anyone reaches for Scheme Pays.
How do I handle mixed NHS and private income?
A salaried GP with additional private sessions, a locum shift here and there, and a share of partnership superannuation creates a genuinely complicated tax picture. Every income stream is reconciled, NHS superannuation is reported correctly, and private income is returned on self-assessment without duplication.
What does our partnership profit share look like on my return?
GP partnership accounts require specific treatment: allocation of notional rent, reimbursed expenses, individual superannuation contributions, and profit shares that change throughout the year when partners join or leave. Partnership accounts and individual returns are prepared as one coordinated piece of work, so nothing is counted twice or missed.
What expenses can I actually claim?
BMA subscription and Royal College fees where they sit on HMRC's approved List 3, noting that the BMA's own entry restricts relief to 85% of the annual subscription, GMC retention, CPD and conference costs genuinely relevant to current practice, home consulting room on a defensible apportionment, professional journals, and motor between surgeries at 55p per mile for the first 10,000 business miles in 2026/27 (up from 45p on 6 April 2026) then 25p. Indemnity needs care: since April 2019 the Clinical Negligence Scheme for General Practice has covered NHS general practice clinical negligence in England at no subscription, so a GP's own MDU, MPS or MDDUS cost is now largely for private and non-clinical work. Prior years are reviewed and amendments filed where the gap is material.
Should my practice incorporate?
Practice incorporation is sometimes the right move for GPs with significant private income outside the partnership and non-working spouse or adult children with pension headroom. It is rarely the right move for a standard salaried or partner GP earning only NHS income. The numbers are modelled before any structural change is recommended.
We have a new partner joining. What are the tax implications?
Admitting a new partner mid-year creates a change-of-basis period, affects the partnership profit shares, and requires careful handling of the incoming partner's NHS pension membership and superannuation contributions. Coordination across all partners is what keeps the transition correct and the returns on time.
How it works
How we work with GP practices, partners and salaried GPs
- 01
GP self-assessment and partnership tax returns
All income streams returned correctly: NHS salary or partnership share, private sessions, locum shifts, rental income, investment income. GP self-assessment filed accurately and inside the deadline. Partner and practice returns are coordinated where both apply.
- 02
NHS pension annual allowance modelling
Your pension input amounts for the NHS Pension Scheme are calculated each year, the tapered annual allowance is modelled against your adjusted income, and Scheme Pays elections are flagged where they may reduce or defer a charge. Modelling is done before the charge crystallises, not after.
- 03
GP partnership accounts preparation
Full practice accounts: income and expenditure analysed by NHS income stream, balance sheet, partner capital and current accounts, notional rent treatment, and a profit allocation that handles mid-year changes in the partner mix. A GP partnership does not file at Companies House, so the outputs that matter are the partnership return to HMRC, the individual partner returns that must agree with it, and the superannuation certificates.
- 04
Medical expense claim review
Current and prior year expense claims are reviewed against HMRC's stated position on medical professional expenses. Where under-claimed amounts turn up, amendments are filed. Going forward, you get a personalised expense guide for your specific role.
- 05
Practice structure advice
Analysis of whether incorporation, a limited liability partnership, or a different profit-sharing arrangement better suits your practice's composition, income mix, and medium-term plans. The tax cost of any structural change is modelled before you commit.
- 06
GP tax planning and annual review
A scheduled call each tax year covering: pension carry-forward headroom, salary and dividend optimisation where relevant, payments on account, upcoming changes to NHS pension regulations, and GP financial planning aligned to your specific practice situation and medium-term goals.
Free calculators
Run the numbers before you send anything
Free to use, on 2026/27 rates. If you want one of our specialists to confirm your figure, say so at the end; you see the result either way.
- NHS Pension Annual Allowance CalculatorEnter your threshold income and annual pension growth from your NHSBSA statement to see your tapered allowance and any potential charge.
- GP Partner Drawings PlannerPlan drawings against profit share, superannuation and the tax set aside for a partner's own return.
- Salaried GP versus PartnerCompare a salaried post with a partnership share on take-home, pension accrual and filing obligations.
Free consultation
Talk to a GP practice accountant
A scoping call with one of our medical accountants. Whether you are enquiring as a practice or as an individual partner or salaried GP, the call covers your current setup, your NHS Pension position, and any expense claims that look under-made. Scope and fees are agreed with you, and enquiring commits you to nothing.
- Medical work onlyNHS pension, practice accounts and private practice
- Read by a medical accountantYour enquiry goes to our accountants who work with doctors
- One position, not threePractice, pension and personal return read together
No obligation. If our specialists think your position is already right, they will tell you so.
Book your free consultation
FAQ
Common questions from GP practices, partners and salaried GPs
Three things. They read NHS income at source, so global sum, Carr-Hill weighting, QOF aspiration and achievement, enhanced services, PCN and DES income and reimbursements are analysed rather than lumped into one figure, and the PCSE statements are reconciled to the ledger. They handle the partnership mechanics: notional rent, capital versus current accounts, and a profit allocation that survives a partner joining or leaving mid-year. And they prepare the superannuation certificates and the individual partner returns as one coordinated piece of work with the practice accounts, so the same income cannot be counted twice or dropped between the two.
Yes, and it is usually the point. The partnership return and every partner's self-assessment have to agree on the profit share, the superannuation deducted and the reimbursed expenses. When the practice uses one firm and the partners use several, the reconciliation is done by nobody and the errors surface at the worst time, typically when someone retires or buys in. Accounting for GP partners works best when the practice figures and the personal figures are prepared against each other.
Yes. From 2023/24 self-employed and partnership profits are taxed on a tax-year basis regardless of the accounting date, so a practice with, say, a 30 June year end now has its profit apportioned across tax years, with transition profits and overlap relief handled in the transition year. The tax bill does not change in total but the timing does, which moves your payments on account. The cash flow effect is worth modelling before it arrives rather than after.
First, verify the HMRC calculation: the NHSBSA issues Pension Savings Statements, but there are known errors in pension input amounts, particularly for members who changed scheme section or had mid-year changes to pensionable pay. If the charge is correct, assess whether a Scheme Pays election makes sense, which defers and capitalises the charge against your eventual pension benefits. Both steps are worked through, in that order.
If you genuinely use a room at home exclusively for NHS or private consulting, a proportion of household costs is allowable. The calculation involves floor area ratios and the proportion of time the room is used professionally. HMRC scrutinises home office claims for GPs, so the claim needs to be defensible. It is documented properly from the outset rather than risking an HMRC challenge later.
From 2023/24 all self-employed income is taxed on a tax-year basis regardless of your accounting year-end, following HMRC's basis period reform. If your practice year-end is not 31 March or 5 April, there will be a transitional overlap profit adjustment to handle in the transition year and going forward. It matters for your payments on account, so the cash flow implications are modelled alongside the tax position.
If you have additional income beyond your salaried NHS pay (private sessions, locum shifts, BMA sessional work, rental income, investment income above the threshold), or if your total income exceeds £100,000 (which triggers the personal allowance taper), then yes. Many salaried GPs think their employer handles everything via PAYE, then face an unexpected self-assessment requirement. Catching it early means registering on time rather than explaining a late return.
Professional clearance with your existing accountant is handled for you and the records requested. Most onboarding is complete within two to three weeks. The work picks up from your current position rather than asking you to restart from scratch. You can switch mid-year without disruption to your filing timeline.