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Bookkeeping & Making Tax Digital for GP Practices
Bookkeeping & Making Tax Digital for GP practices, by specialist medical accountants. Fixed fees. Free quote.
What does bookkeeping & making tax digital for GP practices involve?
Our bookkeeping & making tax digital service for gp practices covers mTD-compatible software set-up, monthly bookkeeping, quarterly submissions. It solves the problems we see most often — gp practices: Quarterly MTD updates from April 2026 on top of a full rota; messy records — 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: Gp practices: Quarterly MTD updates from April 2026 on top of a full rota; messy records.
- Included: MTD-compatible software set-up.
- Included: monthly bookkeeping.
- Included: quarterly submissions.
Free guide: The Doctor's Tax & NHS Pension Handbook 2026/27
Get the free guideWhich accountancy support fits your income?
Start with how you are paid. Different income sources can need different accounts, returns and expense checks.
| How you work | What we check | Support to explore |
|---|---|---|
| Employed or umbrella (PAYE) | Tax codes, eligible employment expenses and whether a tax return is needed. | Healthcare tax refund support |
| Genuinely self-employed | Business income and expenses, Self Assessment and MTD eligibility. | Healthcare Self Assessment service |
| Your own limited company | Company accounts, Corporation Tax, director income and off-payroll status where relevant. | Healthcare limited company accounts |
| Partnership | Practice accounts, allocated profit and each partner’s personal tax position. | Healthcare partnership accounts |
Sound familiar?
Problems we fix for GP partners and practices
- "Our partnership accounts and profit shares are a headache every year."
- "The Type 1 certificate and pension year-end deadline always sneak up on us."
- "I've received an annual allowance charge letter."
- "Partners draw too much and there's nothing left for tax."
- "A partner is leaving and a new one is joining."
- "Reconciling PCN and ARRS funding takes forever."
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
Partnership accounts
Clear profit-share schedules and accounts every partner understands.
Pension certificate service
Type 1 and Type 2 certificates prepared ahead of the deadline.
Drawings planning
Monthly drawings set against a realistic tax reserve.
PCN reporting and payroll
ARRS reconciliation and practice payroll run for you.
How we help
01
MTD-compatible software set-up
Part of our bookkeeping & making tax digital service for gp practices, delivered on a fixed fee.
02
monthly bookkeeping
Part of our bookkeeping & making tax digital service for gp practices, delivered on a fixed fee.
03
quarterly submissions
Part of our bookkeeping & making tax digital service for gp practices, delivered on a fixed fee.
04
receipt capture app
Part of our bookkeeping & making tax digital service for gp practices, delivered on a fixed fee.
Your questions answered
What is Making Tax Digital for Income Tax?
Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Gp practices trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
Want us to check this for you? Get a free review →When do I need to start MTD?
Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Gp practices trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →What software do I need?
Making Tax Digital (MTD) requirements mean many professionals will need MTD-compatible accounting software. From April 2026, this applies to individuals with qualifying income over £50,000. Medical.Accountants works with major cloud-based platforms to streamline your bookkeeping. We recommend the most suitable software based on your practice size and complexity.
Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →What are quarterly updates?
Quarterly updates are digital submissions of income and expenses required under Making Tax Digital for Income Tax. These will be mandatory for qualifying individuals from 6 April 2026. They provide HMRC with a regular summary of your business performance. Medical.Accountants will manage these submissions to ensure your practice remains compliant.
Check the official guidance · www.gov.ukCheck the official guidance · www.gov.ukWant us to check this for you? Get a free review →Can my accountant submit MTD updates for me?
Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Gp practices trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →What records must I keep?
You must keep records of all sales, business expenses, bank statements, and relevant tax documents. Digital record-keeping is increasingly necessary to satisfy MTD requirements. Records should generally be retained for at least six years. Medical.Accountants advises you on the best methods to capture and store these documents efficiently.
Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →How much does MTD bookkeeping cost?
Our packages for gp practices 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.
Check the official guidance · www.gov.ukWant us to check this for you? Get a free review →What happens if I miss a quarterly update?
MTD for Income Tax uses a points-based late-submission regime. HMRC will not award points for missed quarterly updates in the 2026/27 tax year, but you must still submit the updates before submitting your tax return. Later years have different rules. Check the HMRC guidance for your start year; tax return and payment obligations remain.
Check the official guidance · www.gov.ukCheck the official guidance · www.gov.ukWant us to check this for you? Get a free review →How are GP partners taxed on their profit share?
Gp practices pay income tax on taxable profit at 20%, 40% and 45%, plus Class 4 National Insurance on self-employed profit. Payments on account mean your first bill can include half of next year's tax too. Where income also comes from overseas, residence status and split year treatment decide what the UK taxes.
Help with this question: Partnership Accounts for GP Practices
Want us to check this for you? Get a free review →What is a Type 1 pension certificate and when is it due?
GP partners report NHS pensionable profit to the scheme each year on a certificate based on the practice accounts; locum GPs use the locum A and B forms to pay contributions on each piece of pensionable work. Late or wrong forms cause missing service and incorrect pension records. We prepare the figures and check them against the accounts before submission.
Check the official guidance · www.gov.ukHelp with this question: NHS Pension Tax & Annual Allowance for Doctors & Healthcare Professionals
Help with this question: Payroll & Pensions for GP Practices
Want us to check this for you? Get a free review →How much should GP partners set aside for tax from drawings?
GP partners should generally set aside a significant portion of their monthly drawings to cover future tax liabilities. Payments on account are due on 31 January and 31 July each year. Your specific percentage depends on your total earnings and other income sources. We calculate these liabilities in advance to help you manage cash flow.
Help with this question: Partnership Accounts for GP Practices
Want us to check this for you? Get a free review →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 GPs
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 GPs 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 packageLimited company accountants for GPs 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 packagesPersonal tax return packages for GPs
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 packageEmployment 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 GPs
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
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 quoteHow it works
- 01
Free call
A 15-minute chat about your income, structure and deadlines.
- 02
Onboarding in 48 hours
We set up your records, software and HMRC agent access.
- 03
We handle the rest
HMRC, NHS Pensions and every deadline, with reminders before each one.
Free resource
Get the GP year-end deadline calendar free
Tell us where to send it and we'll email it to you.
Your questions, answered
- Do GP practices need bookkeeping & making tax digital?
- Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Gp practices trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
- What does bookkeeping & making tax digital for GP practices include?
- Making Tax Digital for Income Tax applies from 6 April 2026 to sole traders and landlords whose qualifying income (gross self-employment plus property income) is over £50,000, falling to £30,000 from April 2027 and £20,000 from April 2028. PAYE salary does not count. Gp practices trading through a limited company or a partnership are not brought in yet. We set up compatible software and file the quarterly updates for you.
- How much does it cost for GP practices?
- Our packages for gp practices 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 GP practices?
- Many gp practices must file a Self Assessment return: you need one if you have untaxed income such as private, locum or self-employed work. A high PAYE salary alone does not require Self Assessment for 2026/27; check HMRC's current criteria and any notice to file. The online filing and payment deadline is 31 January after the tax year ends. Under the non-MTD rules, late filing normally triggers an initial £100 penalty, with further penalties for longer delays. A different regime applies from the tax year you join MTD for Income Tax.
- 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
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Book a free 15-min tax reviewRelated 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 Making Tax Digital for Income Tax (GOV.UK); HMRC MTD software list; NHSBSA: GP pension certificates (Type 1/Type 2); HMRC partnership guidance (SA800); BMA GP finance guidance; NHS England PCN/ARRS guidance.