GP Practice Accountants

GP PRACTICE ACCOUNTANTS

Specialist accountants for GP practices, GP partners, salaried GPs and primary care networks.

A GP practice is a small business with an unusual balance sheet, an income stream set by contract rather than by market, a partnership deed that governs how profits are split, and a pension scheme that requires its own annual paperwork. Very few practices are the same shape twice.

TaxDigit prepare practice accounts that partners can actually use — profit allocation each partner understands, drawings that do not overshoot, and superannuation figures that reconcile to what the pension agency holds.

What GP practices come to us for

• Annual practice accounts — prepared in the format partners, banks and incoming partners expect.
• Profit sharing and prior shares — seniority, notional rent, out-of-hours and personally-held income allocated in line with the partnership deed.
• Drawings and cash forecasting — monthly drawings set against forecast profit and tax reserves, so nobody has to repay in January.
• Pension certificates — the annual end-of-year certificate for each GP and non-GP partner, and Type 2 returns for salaried GPs.
• Partner changes — joiners, leavers, buy-ins, retirements, mergers and the tax consequences of each.

Our services for GP practices and partners

Practice accounts and partnership tax returns

Full annual accounts, the partnership tax return and each partner’s personal self assessment, prepared together so the figures agree across all of them. We reconcile core contract income, enhanced services, PCN and ARRS reimbursements, dispensing income and premises reimbursements rather than lumping them into one line.

NHS pension: certificates and estimates

GP and non-GP partners each complete an annual certificate of pensionable profits — it is an individual return, not a practice one — and salaried GPs and GPs with pensioned solo income complete a Type 2 self assessment form. These are pension administration returns, nothing to do with HMRC self assessment, and they are due eleven months after the pension year end. We prepare them alongside the accounts so the numbers are consistent and the estimates for the coming year are realistic.

Benchmarking and profitability

Profit per partner, staff cost as a percentage of income, drawings cover and prescribing margins, compared against the practice’s own history so trends are visible before they become problems.

Payroll, pensions and auto-enrolment

Practice payroll including NHS pension contribution tiering, salaried GP contracts, locum reimbursement claims, staff auto-enrolment and year-end reporting.

VAT and dispensing practices

Most primary medical services are exempt from VAT, but a dispensing practice makes taxable supplies too, which brings partial exemption and the ability to recover a proportion of input tax — frequently including VAT on premises costs. Getting the method right is worth real money and is regularly missed.

Premises, borrowing and notional rent

Accounts and projections for surgery purchases, refurbishment borrowing, notional and cost rent reimbursement, and the personal tax position of partners who own the premises.

Making Tax Digital for Income Tax

Making Tax Digital for Income Tax applies from 6 April 2026 where qualifying income exceeds £50,000, extending to over £30,000 from April 2027 and over £20,000 from April 2028. Partners with property income or private work alongside the practice are the ones most likely to be caught first. We get the record keeping ready ahead of the deadline rather than during it.

Who we act for in primary care

• GP partners and partnerships — single-handed practices through to large multi-site partnerships.
• Salaried GPs — tax returns, expense claims, Type 2 forms and advice on becoming a partner.
• Locum GPs — structure, pensioning locum work and IR35.
• Primary care networks and federations — income allocation between member practices, ARRS staff costs and governance of shared funds.
• Non-GP partners and practice managers — pension certificates and remuneration planning.
• Dispensing practices — stock, margins and VAT partial exemption.

Why practices choose TaxDigit

• Chartered certified accountants who work with clinicians daily, not once a year.
• Accounts explained to the partnership in a meeting, not emailed as a PDF.
• Fixed fees agreed in advance, with year-round access rather than per-question billing.
• Guildford-based, acting for practices across Surrey, London and the UK.

Frequently asked questions

What does a GP practice accountant do that a general accountant does not?

Three things in particular: allocate profits in line with a partnership deed that includes prior shares and personally-held income, prepare the NHS pension certificates that sit alongside the accounts, and handle the partial exemption calculation for dispensing practices. Each of those is specialist, and each is where errors tend to be found.

Who completes the annual pension certificate — the practice or the partner?

Each GP partner and non-GP partner completes their own certificate of pensionable profits. It is an individual return even though the underlying figures come from the practice accounts. Salaried GPs and GPs with pensioned solo income complete a Type 2 form instead.

When are the Type 1 and Type 2 forms due?

Eleven months after the end of the pension year — in other words, by the following 28 February. We prepare them from the practice accounts so the pensionable profit figures reconcile rather than being estimated twice.

How should we set partner drawings?

From a forecast, not from last year’s profit. We set monthly drawings against projected profit with tax and superannuation reserved separately, and review at the half-year. Practices that draw against last year’s accounts are the ones that end up asking partners for money back.

Can a dispensing practice recover VAT?

Partly. Dispensing is a taxable supply while primary medical services are exempt, so a dispensing practice is partially exempt and can recover a proportion of its input tax — often including VAT on significant premises and refurbishment costs. The recovery method matters and is worth reviewing if it has not been looked at recently.

What happens to the accounts when a partner joins or retires?

The profit share has to be apportioned across the year, capital and current accounts settled, the pension certificates split, and the incoming partner’s buy-in accounted for. We handle the mechanics and set out what each partner personally will owe or receive, before it happens rather than afterwards.

Can you act for our PCN as well as the practice?

Yes. Networks raise their own questions about how income and ARRS staff costs are allocated between member practices and how shared funds are governed. We can act for the network, the practices, or both where there is no conflict.

Do you act for practices outside Surrey?

Yes. We are based in Guildford and act for practices across the UK. Accounts meetings work perfectly well by video, and most of the year’s work is done on documents rather than in person.

Information correct as at 12 August 2026. This page is general information about UK tax and NHS pension administration and is not advice for any particular practice or individual; rules change and circumstances differ. Please speak to us before acting on anything you read here.