SME Accounting News & Deep Dives: HMRC Agent MFA Rollout, Timely Tax Payments from 2029 & the 5 October Self Assessment Deadline
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Wednesday 16 September 2026 edition | Author: Jessica
HMRC’s final agent account security rollout begins in less than two weeks, while proposed changes to Income Tax payment timings could alter how some directors and SME owners manage personal tax from 2029.
This week also brings important reminders about the 5 October Self Assessment registration deadline, the next MTD quarterly update, Corporation Tax rates and the Autumn Budget.
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1. HMRC agent MFA rollout begins on 28 September
HMRC’s final phase of mandatory multi-factor authentication (MFA) for agent accounts will take place between 28 September and 15 October 2026.
MFA adds another security step when an accountant or tax agent signs into HMRC’s online services. Instead of using only a Government Gateway ID and password, the user must also enter a one-time access code.
This matters to SME owners because many companies rely on an accountant to file Corporation Tax returns, manage payroll, submit VAT returns or deal with Self Assessment for directors. If an accountant’s access is disrupted, routine compliance work could be delayed.
HMRC is expected to activate accounts without giving each agent a specific date. Activation will take place between 8am and 9am, Monday to Thursday. If MFA has not been activated by 9am on a particular day, it should not be switched on later that day.
Practical steps for SME owners and directors
Ask your accountant to confirm that they have:
- Checked and updated the contact details connected to the agent account.
- Reviewed existing MFA options and removed outdated access methods.
- Set up an authenticator app rather than relying only on SMS.
- Arranged for more than one administrator to have appropriate access.
- Confirmed that the software used for online filing remains compatible.
- Tested the sign-in process before the rollout window begins.
An authenticator app is generally preferable because it does not depend on mobile signal or delivery of a text message. More than one administrator is also important. If a single person leaves the firm or loses access to their device, another authorised user should still be able to manage the account.
For businesses that manage some submissions themselves, it is worth checking who controls the relevant HMRC access and whether a second administrator is in place.
2. Timely Payments proposals could bring personal tax closer to real time
HMRC’s Timely Payments in Income Tax Self Assessment (ITSA) consultation considers how taxpayers could pay Income Tax closer to when income is earned.
At present, some taxpayers can face a gap of up to 22 months between earning income and paying the associated tax. This can create a large first tax bill, followed by payments on account, and may cause cash-flow pressure for growing businesses.
The proposals are intended to apply from April 2029, although they are not law at this stage.
How the proposed system could work
For taxpayers with sufficient PAYE income, HMRC plans to collect forecast ITSA liabilities through PAYE coding adjustments. This could mean tax being deducted during each pay period rather than being paid through the traditional January and July timetable.
For other taxpayers, including those without enough PAYE income, HMRC is exploring more frequent direct payments on account. These could be monthly or quarterly.
The proposals would not increase the total tax due. They would change the timing of payments. Taxpayers would still complete a Self Assessment return and reconcile the forecast payments against their actual liability.
Why directors and SME owners should take notice
A limited company director may have a personal tax liability arising from dividends, property income, freelance work or other sources. A director with a PAYE salary and additional taxable income could therefore be affected if the proposals become law.
The transition period may be particularly important. Taxpayers could have payments relating to an earlier year alongside payments towards the current year. That could temporarily increase the amount leaving the household or business each month.
The practical action now is to improve forecasting. Keep business and personal tax reserves separate, review expected dividends before they are declared and include possible personal tax payments in your cash-flow planning.
A suitable business accountant UK service can help directors understand how salary, dividends and other income interact before payment timing changes are introduced.
3. New Self Assessment filers have until 5 October 2026
Anyone who needs to file a Self Assessment tax return for the 2025/26 tax year but has not filed one before generally needs to tell HMRC by 5 October 2026.
That date is now roughly three weeks away.
This is the registration deadline, not the deadline for submitting the tax return itself. The online filing deadline for the 2025/26 return is 31 January 2027.
HMRC has improved its online registration service. New users registering online should receive their Unique Taxpayer Reference (UTR) in their HMRC online account within about 72 hours, rather than waiting for a postal letter.
You can check the official dates using the GOV.UK Self Assessment deadlines reference.
If you are a company director, check whether your salary, dividends or other income means you need to file. Do not assume that having an accountant for your limited company automatically means your personal Self Assessment position has been reviewed.
4. MTD for Income Tax: 7 November quarterly update reminder
The first MTD for Income Tax cohort includes unincorporated businesses and landlords with qualifying income above £50,000.
The next quarterly update deadline is 7 November 2026. This usually covers the second quarter of the 2026/27 tax year, depending on the accounting or reporting basis being used.
HMRC has confirmed that there will be no penalty points for late quarterly updates during 2026/27. However, the reporting obligation still applies. Late annual Self Assessment returns and late tax payments can still attract penalties.
The next wave begins in April 2027 for taxpayers with qualifying income over £30,000, based on their 2025/26 figures.
Limited companies are not themselves brought into MTD for Income Tax simply because they are incorporated. However, a director or owner may have separate personal income that requires attention. Review the position early if you have more than one income source.
5. Corporation Tax rates remain unchanged for 2026
For the financial year beginning 1 April 2026, the Corporation Tax structure remains:
- 19% small profits rate for profits up to £50,000.
- 25% main rate for profits over £250,000.
- Marginal relief for profits between £50,000 and £250,000.
Within the marginal relief band, the effective marginal rate is commonly stated as 26.5%. This means the overall Corporation Tax rate increases gradually between the small profits and main rate thresholds.
The thresholds are reduced where a company has associated companies. They can also be proportionately reduced for short accounting periods.
Growing SMEs should not look only at the headline percentage. Profit extraction, associated companies, accounting dates and planned investment can all affect the final calculation. Corporation tax accountants can help model different scenarios before year-end decisions are made.
6. Autumn Budget countdown: 28 October 2026
The Autumn Budget is scheduled for 28 October 2026.
Before then, SME owners should prepare updated cash-flow forecasts, review outstanding tax liabilities and identify decisions that may need to be made before or after the Budget.
Do not make dividend, salary or remuneration decisions based on rumours. Wait for confirmed announcements and obtain advice on how any changes apply to your company and personal position.
SME action checklist
Before the next edition, consider whether you should:
- Ask your accountant about HMRC’s MFA activation process.
- Check that the firm has current contact details and more than one administrator.
- Use an authenticator app and test access before 28 September.
- Review personal tax reserves in light of the proposed 2029 changes.
- Confirm whether you or a director must register for Self Assessment by 5 October.
- Prepare records for the 7 November MTD quarterly update if you are in scope.
- Check 2025/26 qualifying income to assess potential MTD obligations from April 2027.
- Review Corporation Tax projections, especially if profits are near £50,000 or £250,000.
- Update cash-flow forecasts ahead of the Autumn Budget.
Self-Assessment tick-box instruction and SA form
If you need help with personal tax, complete the Accountant Search SA form and tick the Self-Assessment box. This tells us that you need support with a Self Assessment return or related personal tax issue.
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You can also use the Accountant Search form to provide your details. The platform is not an accountancy practice; it helps individuals and businesses connect with accountants who may be able to provide accounting and tax services.
For context, see our Monday 14 September SME Accounting News & Deep Dives edition and the 11 September 2026 SME tax update.
Disclaimer: This article reflects the position understood as at 16 September 2026. The Timely Payments measures are proposals and may change before legislation is introduced. Tax outcomes depend on individual and company circumstances. Obtain professional advice before acting.