Staying compliant: HMRC deadlines, record-keeping and digital accounting for dental practices

Dental practice compliance has grown considerably more demanding over the past decade. HMRC deadlines, digital record-keeping requirements, quarterly reporting under Making Tax Digital, and the expanding list of software-based submission obligations all need managing alongside the clinical work. Unlike a missed appointment, a missed HMRC deadline triggers an automatic penalty with no warning and no grace period.

For the full picture across tax, payroll and compliance, see the complete guide to dental accounting and tax.

What this article covers

• The HMRC deadlines dental practices must hit and what happens when they do not.
• Record-keeping: what HMRC actually expects and for how long.
• Making Tax Digital for VAT (already compulsory) and for Income Tax (live from April 2026).
• The three things dental associates consistently get wrong about MTD.
• Accounting software and which options dental practices in the UK actually use.

The compliance failure that one habit prevents

Charles Suthakran, Business Development Executive, Accountancy and Tax at Samera, on the single most common compliance failure he sees across dental practices, and the one thing that eliminates it:

“One business account, one business card, used for nothing else. It sounds almost too basic to be worth saying, but it’s the single thing that causes the most trouble, and it’s entirely avoidable. What happens in practice is that one account ends up doing two jobs, the practice’s and the owner’s. A card gets used for stock and for the weekly shop.

Money moves between personal and business without anyone noting why. It reconciles fine day to day, so nobody worries about it. The problem only shows up when HMRC asks a question, because at that point you have to prove a cost was a business cost, and you can’t cleanly do that if it’s tangled up with personal spending. A legitimate claim you’re fully entitled to gets disallowed simply because you can’t evidence it. Keep the two completely separate from day one, and most of that risk just disappears.”

Charles Suthakran
Dental Accountant

HMRC deadlines dental practices must meet

Self Assessment for associates and sole traders

• 31st January: online Self Assessment return deadline, plus any tax owed for the previous year.
• 31st July: second payment on account.
• 5th October: deadline to register for Self Assessment if newly self-employed.

Missing the 31 January deadline triggers an automatic £100 penalty from the moment it passes, regardless of whether you owe any tax at all. Further charges apply at three months, six months, and twelve months late. Interest runs on any unpaid tax from the due date.

Self Assessment deadlines: gov.uk

The payments on account issue

Payments on account are advance payments towards next year’s tax bill, 50% due in January alongside the current year’s bill, and 50% in July. In a high-earning year you could effectively be paying two years’ worth simultaneously. Set aside a monthly percentage from the start of self-employment. Full details are in our article on taxes for dental associates.

Corporation Tax for limited companies

• Payment: nine months and one day after the accounting year-end.
• CT600 return: twelve months after the accounting year-end.

Filing the CT600 late triggers an automatic fixed penalty even if no tax is owed, rising in stages the longer it’s left, with a further surcharge added on any unpaid tax once you’re six and twelve months late. Repeated late filing increases the fixed penalties further. Paying the tax late is a separate matter and triggers daily interest from the day after the due date, regardless of whether the return itself was filed on time.

Corporation Tax deadlines: gov.uk

VAT returns

VAT-registered practices submit quarterly returns due one month and seven days after the end of each VAT period. Manual submissions through HMRC’s old online portal are no longer accepted. Everything must go through MTD-compatible software.

A late submission adds a penalty point rather than an immediate fine, and once you reach the threshold for your filing frequency, a fixed penalty applies, repeating for every late submission after that until compliance is restored. Late payment is penalised separately and depends on how many days late the payment is, alongside interest that runs from day one until the VAT is paid in full.

VAT: gov.uk

Payroll deadlines

• RTI submissions: on or before every single payday. Not monthly. On or before each pay date.
• P60s: issued to all employees by 31st May.
• P11Ds: submitted to HMRC by 6th July.
• Class 1A NI: due 19th July, or 22nd July for electronic payment.

Missing an RTI deadline triggers a monthly late filing penalty, scaled to the number of employees in the PAYE scheme. The first missed submission in a tax year usually goes unpenalised, but persistent late filing brings a further charge on the tax and National Insurance that should have been reported.

Running payroll: gov.uk

Record-keeping: what HMRC expects

HMRC can open an enquiry into any return at any time. If supporting records cannot be produced, expense claims can be disallowed and estimated assessments raised. Good record-keeping is not administrative tidiness for its own sake, it is what lets you defend what you have filed.

• NHS income records: remittance statements, schedule of fees, UDA reports.
• Private income records: fee schedules, receipts, patient billing.
• Business expense records: lab invoices, CPD receipts, indemnity premiums, travel logs, staff costs.
• Equipment purchase invoices for all capital items, needed for capital allowance claims.
• Payroll records: payslips, P60s, P11Ds, and all RTI submissions.
• VAT records: all invoices in and out and evidence for exempt and zero-rated claims.
• Bank statements for every business account.
• Associate agreements and fee records.

How long to keep records

• Self-employed individuals: at least five years after the 31st January filing deadline for the relevant tax year.
• Limited companies: at least six years from the end of the relevant accounting period.
• VAT records: at least six years.

Record-keeping requirements: gov.uk

What actually happens during an HMRC enquiry

Charles on what triggers most enquiries and how the outcome differs completely based on whether records exist:

“The enquiries I see rarely start with anything dramatic. It’s usually a figure that looks out of step, margins that don’t sit right for the size of the practice, a sharp swing in costs year on year, or private income that looks light against the number of surgeries running. That’s often enough for HMRC to open a check and start asking for the records behind the numbers.

What they’re really testing is whether what’s on the return can be backed up. And that’s where the two types of practice split completely. The one with clean, current records hands over the bank statements, the invoices, the payroll, all tied together, and the enquiry tends to be short and uneventful, because there’s nothing to find and everything to show.

The one without spends weeks reconstructing a year they should have recorded as it happened, and every gap gets read in HMRC’s favour, not theirs. Same underlying business, often the same actual tax position, but a totally different experience, and a totally different bill once disallowed costs and penalties are added. The records don’t change what’s true. They change whether you can prove it.”

Charles Suthakran
Dental Accountant

Making Tax Digital

MTD for VAT: already compulsory

All VAT-registered businesses have been required to follow MTD rules for VAT since April 2022. For dental practices that are VAT-registered because they provide cosmetic or other taxable services, VAT records must be kept digitally and returns must be submitted through MTD-compatible software. The old HMRC online portal no longer accepts submissions.

MTD for VAT: gov.uk

MTD for Income Tax Self Assessment: live from April 2026

This is the change that affects most dental associates, and it is rolling out in stages by income threshold over the next two years. Charles on the three misunderstandings he sees most consistently when he talks to associates about it:

“The reaction is usually one of two things: either they’ve never heard of it, or they assume it’s been pushed back again and isn’t really happening. It’s been delayed so many times that there’s a fair bit of ‘I’ll believe it when I see it.’ But for associates earning over £50,000, it’s live now, and that’s most of them. The misunderstandings are consistent.

The biggest one is that they think quarterly updates mean paying tax four times a year, they don’t. The payment dates haven’t changed at all. The updates are just summaries of income and expenses sent throughout the year. The second is that they assume they can carry on handing everything over in a carrier bag in January. That stops working, because the records now have to be kept digitally in compatible software as you go.

And the third is the threshold itself: it’s on gross income, your total billings, not your take-home profit. An associate billing £90,000 who thinks of their income as the £55,000 that lands in their account assumes they might be under the threshold. They’re not. There is a soft landing in the first year where HMRC won’t issue penalty points for late quarterly updates, but I’d treat that as breathing room to get the system right, not a reason to ignore it.”

Charles Suthakran
Dental Accountant

For exact income thresholds, quarterly submission dates, and what the digital record-keeping and final declaration requirements involve, see our dedicated Making Tax Digital page.

Accounting software dental practices actually use

For a full comparison of software options and how they match to different practice types, see our bookkeeping article.

In short: Xero is the most widely used platform in UK dentistry and the one Samera uses for dental finance automation. QuickBooks is popular with associates and smaller practices. Sage is more common in larger practices and groups with complex payroll requirements. Hubdoc works alongside Xero for document management. All four are MTD-compatible.

Practical steps for staying compliant

• Move to cloud accounting software. Paper records and spreadsheets are not sufficient for MTD compliance.
• Review your financial position monthly rather than only at year-end.
• Keep business and personal finances completely separate from day one.
• Plan for tax monthly. Setting aside income every month makes January and July payment dates far less stressful.
• Work with an accountant who understands dental practice specifically, not just general small business accounting.

Compliance is a habit, not a deadline

Most of what causes trouble in this article traces back to the same root cause: things get sorted after the fact instead of as they happen. A missed deadline is rarely about the date itself, it’s about records or payments not being ready when the date arrived. An HMRC enquiry rarely starts with anything dramatic, it starts with a figure that doesn’t add up because the paper trail behind it was never kept properly.

The single change that prevents the most common problem, keeping one business account and card completely separate from personal spending, costs nothing and takes no expertise. The same is true of moving to digital records before MTD forces the issue, rather than after.

None of this requires getting every deadline memorised. It requires a system, cloud software, monthly reviews, and an accountant who knows dental practices specifically, that keeps you ahead of what HMRC expects rather than reacting to it.

Dental Tax and Accounts Compliance: FAQs

Glossary

• RTI (Real Time Information) – HMRC’s system requiring employers to report pay and deductions on or before each payday, rather than at year end.
• CT600 – The Corporation Tax return a limited company must file with HMRC, due twelve months after the accounting year-end.
• P60 – The annual summary of an employee’s total pay and deductions for the tax year, issued to all employees by 31 May.
• P11D – The form reporting benefits in kind provided to employees, submitted to HMRC by 6 July.
• Class 1A National Insurance – Employer-only National Insurance contributions due on benefits in kind, paid by 19 July (or 22 July electronically).
• Self Assessment – The system through which self-employed individuals report income and calculate tax owed, with an annual return due by 31 January.
• Payments on account – Advance payments towards next year’s Self Assessment tax bill, due in January and July, based on the previous year’s liability.
• Penalty points – HMRC’s system for late submissions, where each late return adds a point rather than an immediate fine. A financial penalty applies once a threshold is reached, and repeats for each further late submission until compliance is restored.
• MTD (Making Tax Digital) – HMRC’s requirement to keep digital records and submit returns through compatible software, already compulsory for VAT and rolling out for Income Tax Self Assessment from April 2026.

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