MTA
Medical Tax Accountants
Specialist accountants for GP partners

Partnership finance,
from someone who lives it.

Practice accounts, partnership tax, pension certificates and annual allowance — handled by a firm founded by a practising GP partner who deals with the same numbers you do.

The GP partner tax problem

Being a partner means your pay, your tax and your pension stop being simple.

A GP partner isn't an employee — you're a self-employed business owner whose income moves with the practice, whose tax runs a year behind, and whose NHS pension needs an annual reconciliation most accountants have never prepared.

Drawings aren't your pay

You're taxed on your profit share, not the monthly drawings that land in your account. When the practice does better than forecast, the tax bill follows — often eighteen months later. Without regular forecasting, partners get blindsided.

Type 1 pension certificates

Every GP partner must file an annual Certificate of Pensionable Profits with PCSE by 28 February. It depends on finalised practice accounts and your profit share — and it's a form most general accountants have simply never seen.

Annual allowance tax traps

NHS pension growth plus a good profit year can quietly push you over the tapered annual allowance — triggering tax charges partners often only discover when it's too late to plan. This needs reviewing every single year.

How we help GP partners

Everything a GP partner actually needs, in one place.

We work exclusively with medical professionals — and the firm is run by a practising GP partner. Partnership accounts, profit shares and pension certificates aren't a specialism we dabble in. They're the day job.

Practice accounts

Full partnership accounts covering GMS/PMS contract income, enhanced services, QOF, reimbursements and staff costs — prepared to the standard lenders and incoming partners expect.

Partnership & personal tax returns

The partnership return, plus each partner's self-assessment with payments on account managed — filed early so every partner knows their January bill months in advance.

Type 1 pension certificates

Annual Certificates of Pensionable Profits prepared from the practice accounts and filed with PCSE by the 28 February deadline — for every partner, every year, as standard.

Annual allowance reviews

Yearly review of your pension growth against the tapered annual allowance, with Scheme Pays elections prepared where a charge arises — before the deadline, not after it.

Partner changes

Admissions, retirements and profit-share changes handled properly — capital accounts, current accounts, tax elections and pension implications all dealt with at the right time.

Profit forecasting & drawings

Quarterly profit forecasts so drawings stay aligned to what the practice is actually earning — and no partner faces a January tax bill their drawings never provided for.

The big decision

Salaried GP or GP partner?

For many GPs the biggest financial decision of their career. Below is the honest side-by-side — the right answer depends on the practice, the deal on the table, and what you want the next ten years to look like.

Salaried GP
GP Partner
How you're paid
Fixed salary through PAYE. Predictable, taxed at source.
Profit share. Monthly drawings against your share of practice profits — income moves with practice performance.
How you're taxed
PAYE handles it. Little to do beyond checking your code.
Self-employed. Self-assessment with payments on account — tax arrives in lumps, roughly a year behind the income.
Earning potential
Capped by the contract. Sessions × rate.
Higher on average — partners share in the practice's whole performance, including enhanced services and efficiencies.
Risk
Low. Employment rights, sick pay, fixed income.
Real. Unlimited liability for the practice's obligations, income risk, and capital tied up in the business.
NHS Pension
Contributions deducted through payroll. Officer-style administration.
Type 1 practitioner. Pensionable profits reconciled annually by certificate — and annual allowance needs active management.
Say in the practice
Limited. You work within decisions others make.
Full. You own the business — staffing, premises, strategy, and the rewards or consequences.
The honest answer: partnership usually pays more, but it pays differently — irregularly, a tax year in arrears, and with genuine business risk attached. The deciding factors are usually the health of the specific practice, the premises arrangement, and your appetite for running a business alongside practising. If you're weighing up an offer, we'll go through the practice accounts with you before you sign anything.
NHS Pension Type 1

The certificate every partner must file.

Every GP partner in the NHS Pension Scheme must complete an annual Certificate of Pensionable Profits — commonly called the Type 1 certificate. It reconciles the pension contributions collected through the practice against your actual pensionable profits once the accounts are finalised.

Because pensionable profit depends on the practice accounts, your profit share, and adjustments for non-NHS income, the certificate can't be done in isolation — it has to be prepared alongside the practice accounts and your personal tax return. Get it wrong and your pension record is wrong, which quietly follows you all the way to retirement.

What we do:

  • Prepare the certificate from the finalised practice accounts so pensionable profit, added years and contribution tiers are calculated correctly.
  • Submit to PCSE by the 28 February deadline — for every partner in the practice where we act for the partnership.
  • Reconcile contributions collected vs due, so under- or over-payments are corrected rather than compounding year after year.
  • Check the position against your pension record and chase PCSE where the record doesn't reflect what's been filed (it happens more than it should).

Behind on certificates from previous years? That's common — and fixable. We can work through prior-year certificates and bring your pension record fully up to date.

Annual allowance & expenses

The bits that catch partners out.

Annual allowance & Scheme Pays

NHS pension growth is measured against the annual allowance each year — and for higher-earning partners the allowance tapers down, so a strong profit year can create a pension tax charge on top of the income tax bill.

The charge can often be settled through a Scheme Pays election, where the NHS scheme pays it in exchange for a reduction to your future pension — but the election has a hard deadline, and deciding whether it's the right move needs your growth figures, not guesswork.

We review your pension savings statement and taper position every year, quantify any charge, and prepare the Scheme Pays election where it makes sense — before the window closes.

What partners can claim personally

Beyond practice-level expenses, GP partners can typically claim personally for:

  • Medical indemnity (MDU, MPS, MDDUS) where not paid by the practice
  • GMC and Royal College fees
  • Professional subscriptions (BMA, journals)
  • Courses, CPD and appraisal costs
  • Business mileage (home visits, branch surgeries — not home to work)
  • Home-office costs where practice work is done at home
  • Equipment used for practice work
  • Accountancy fees for your personal tax work
Frequently asked

Questions GP partners ask us.

What is the Type 1 Certificate of Pensionable Profits and when is it due?
The Type 1 annual certificate is the form every GP partner must complete to reconcile their NHS Pension contributions against their actual pensionable profits for the year. It's submitted to Primary Care Support England (PCSE) and is due by 28 February following the end of the relevant tax year. Because it depends on finalised practice accounts and your profit share, it needs to be prepared alongside your personal tax work — we handle both together.
How is a GP partner taxed?
GP partners are self-employed. You're taxed on your share of the practice profits — not on your drawings. The partnership submits a partnership tax return, and each partner reports their profit share on their personal self-assessment, paying income tax and Class 4 National Insurance through payments on account. From 2024/25 partners are taxed on the tax-year basis following basis period reform.
What's the difference between drawings and profit?
Drawings are the monthly cash you take from the practice; profit is your share of what the practice actually earned. Tax is charged on profit, not drawings. If the practice performs better than expected, your tax bill can be higher than your drawings suggest — which is why partners need regular profit forecasts, not just year-end accounts.
The practice already has an accountant — do I need my own?
The practice accountant acts for the partnership as a whole, and typically prepares the practice accounts and partnership return. Your personal tax return, pension certificates, annual allowance position and personal expense claims are your own responsibility. Many partners use the practice accountant for both; others prefer independent advice on their personal position — especially around pension tax. We can act for the practice, for you personally, or both.
I'm about to become a GP partner — what changes financially?
Almost everything: you become self-employed, pay tax through payments on account, take drawings rather than a salary, may buy into the practice's working capital or premises, and move to Type 1 NHS Pension arrangements. The first eighteen months are where most new partners get caught out on cash flow — we map the whole transition before you sign the partnership deed. Coming from locum work? Start with our locum GP accountants page.
What can I do about annual allowance tax charges?
Higher-earning partners are frequently affected by the tapered annual allowance, and NHS pension growth can trigger unexpected charges. Options include Scheme Pays elections (the NHS scheme settles the charge from your future pension), reviewing pensionable income, and planning around profit fluctuations. We review your position annually using your pension savings statements — before the Scheme Pays deadline, while there's still time to act.
Should I buy into the surgery premises?
Premises ownership can be a sound long-term investment — notional rent or cost rent reimbursement often services the borrowing — but it concentrates risk and complicates retirement, as outgoing partners must be bought out. The answer depends on the practice's property arrangements, your time horizon and the mortgage terms available. We model the numbers on both sides before you commit.
Can our practice switch its accounts to you?
Yes. We handle the professional clearance letter and records transfer from your current accountant, and most practices switch within a few weeks with no disruption to payroll or filings. Because we work exclusively with medical professionals, practice accounts, GMS and PMS income streams, and partner pension certificates are our day-to-day work — not an occasional job.
Does Making Tax Digital affect GP partners?
Not yet for partnership income — Making Tax Digital for Income Tax currently applies to sole traders and landlords, and partnerships are due to join at a later date still to be confirmed. But if you have self-employed income outside the practice — locum sessions or private work over £50,000 gross from April 2026, £30,000 from April 2027 — that income brings you into MTD now, with digital records and quarterly updates to HMRC. Either way the direction of travel is digital, and partners who move early avoid the scramble.
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