Can HMRC check more than one tax at the same time

Q: Does each tax keep its own rules?

Yes, and this is where combined checks catch people out. Corporation tax and income tax returns are examined through an enquiry opened within the enquiry window, or later only by discovery. CH206600 says that where the window for a period has closed, HMRC can address a risk only if there is a potential discovery position. See the enquiry window for tax returns. VAT and PAYE have no self assessment enquiry framework. CH206600 says that where risk information is used for checks into taxes without that framework, no enquiry needs to be opened, but if the risk extends to income tax or corporation tax an enquiry may then be needed. VAT checks are covered in our VAT compliance check guide. Information notices are restricted for filed returns. Paragraph 21 of Schedule 36 stops a taxpayer notice being given to check the income tax or corporation tax position for a period covered by a return unless a condition is met. Two of those conditions are directly relevant to combined checks: condition C, where the information is also required to check a tax other than income tax, capital gains tax or corporation tax (such as VAT), and condition D, where it is required for checking PAYE or CIS deductions. The practical effect is that records requested for a VAT or PAYE check can be obtained even when the corporation tax enquiry window is closed. CH206500 notes that income tax and corporation tax officers may need their VAT colleagues to review earlier years unless they can use discovery.

Q: How might a combined check play out?

Illustration only. A VAT officer visiting a small restaurant company notices that card takings in the till reports are higher than the sales in the VAT returns. The director drives an expensive car that the declared profits do not seem to fund. The VAT officer can use Schedule 36 to obtain the till and bank records for the VAT check and assess underdeclared VAT, back 4 years if not deliberate. The officer refers the corporation tax and director risks across. If the corporation tax enquiry window for the latest return is open, HMRC opens an enquiry; earlier years need discovery. If the missing takings were extracted by the director, HMRC opens a linked enquiry into the director's return with a separate notice, and an employer compliance review may follow. Each tax produces its own assessment or amendment, appeal route and penalty, but the case may be settled together.

Yes. HMRC can coordinate or combine compliance checks into VAT, PAYE, corporation tax and a director’s own income tax, and its guidance actively encourages this cross tax working. But each tax is still checked under its own rules: a corporation tax or income tax return can only be examined through an enquiry or a discovery assessment, VAT and PAYE have no enquiry window, and the time limits for assessing each tax are different.

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Can one HMRC check really cover several taxes?

It can. HMRC’s Compliance Handbook at CH205100 says compliance checks sometimes involve cross tax working, meaning looking into more than one tax position, and that all officers doing compliance checks should be aware of other taxes and refer on any risks they find. CH206500 says the information and inspection powers in Schedule 36 to Finance Act 2008 enable HMRC to coordinate and combine compliance checks into different taxes when that is the quickest and most efficient way to address risks.

The same guidance lists the benefits HMRC sees in this approach: pooling risk information and expertise, joint meetings and inspections, coordinated requests for information, and a fuller body of evidence on which to judge behaviour for penalty purposes. A cross tax case can start because HMRC’s risk teams flag several risks at the outset, because an officer spots a risk in another tax during their own check, or because another caseworker refers one across. For example, a VAT officer may decide there is also an income tax risk.

At the start of a cross tax check HMRC should send the appropriate cross tax letter. When officers from different disciplines visit or meet you together, CH206500 says they must explain who they are, which taxes they are asking about and under what legislation they are acting.

What powers let HMRC look at more than one tax?

The main power is Schedule 36 to Finance Act 2008. Paragraph 1 lets an officer require information or documents reasonably required for checking your tax position. Paragraph 63 defines “tax” for this purpose to include, among others, income tax, capital gains tax, corporation tax and VAT. Paragraph 64 defines your tax position widely, covering past, present and future liability, penalties, and claims and elections, and paragraph 64(2) extends it to deductions you must make under the PAYE regulations and the Construction Industry Scheme.

So one information notice can, in principle, ask for records relevant to several taxes at once. CH206500 adds a limit on the officer’s side: they must use only the powers relevant to the tax being checked, and must not attempt to deal with technical risks in a tax they are not trained in. Our page on the Schedule 36 information notice explains appeals and what can be refused.

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How does a check into a company link to the director’s personal tax?

HMRC treats them as separate taxpayers. EM8004 says a company is a legal entity separate from its shareholders and directors, and that although a company enquiry may extend to the affairs of participators and directors and to the company’s duties as an employer, each part must be conducted under the legislation, guidance and codes of practice that apply to that part.

In practice this means separate notices. EM8210 says HMRC must issue a separate enquiry notice to each director whose return it needs to examine, together with factsheet CC/FS1, and that the officer running the company enquiry should normally take ownership of the linked director enquiries so that they are not closed prematurely. EM8220 says that HMRC should not settle a linked director enquiry by contract or formal closure before it has a signed contract from the company, because that would rule out alternative recovery from the director.

Where does PAYE fit in?

Employer obligations are checked separately from the company’s corporation tax return. EM8004 points out that the returns a company makes as an employer and contractor are not self assessment returns, and that employer compliance work does not affect the corporation tax enquiry position. EM8250 says employer compliance staff confine their questions to employer obligations, always seek clearance from the corporation tax officer before opening a review, and use Schedule 36 powers.

The settlement can still be brought together. EM8250 explains that PAYE and NIC irregularities are broadly recovered from the company by a Class 6 settlement, and that this can be included in the company’s corporation tax contract offer or sought as a separate offer. Director benefits are usually dealt with by assessment or settlement with the director personally. See our guide to the HMRC employer compliance check.

Does each tax keep its own rules?

Yes, and this is where combined checks catch people out.

Corporation tax and income tax returns are examined through an enquiry opened within the enquiry window, or later only by discovery. CH206600 says that where the window for a period has closed, HMRC can address a risk only if there is a potential discovery position. See the enquiry window for tax returns.
VAT and PAYE have no self assessment enquiry framework. CH206600 says that where risk information is used for checks into taxes without that framework, no enquiry needs to be opened, but if the risk extends to income tax or corporation tax an enquiry may then be needed. VAT checks are covered in our VAT compliance check guide.
Information notices are restricted for filed returns. Paragraph 21 of Schedule 36 stops a taxpayer notice being given to check the income tax or corporation tax position for a period covered by a return unless a condition is met. Two of those conditions are directly relevant to combined checks: condition C, where the information is also required to check a tax other than income tax, capital gains tax or corporation tax (such as VAT), and condition D, where it is required for checking PAYE or CIS deductions.

The practical effect is that records requested for a VAT or PAYE check can be obtained even when the corporation tax enquiry window is closed. CH206500 notes that income tax and corporation tax officers may need their VAT colleagues to review earlier years unless they can use discovery.

Are the time limits the same for every tax?

No. The Compliance Handbook tables set them out tax by tax:

Tax	Normal	Careless	Deliberate
Income tax and CGT (TMA 1970 ss34 and 36)	4 years from end of tax year	6 years	20 years
Corporation tax (FA 1998 Sch 18 para 46)	4 years from end of accounting period	6 years	20 years
VAT (VATA 1994 s77)	4 years from end of the VAT period	4 years (no extension)	20 years
PAYE determinations	Same limits as income tax discovery assessments (CH56100)

CH56300 also says a VAT assessment made more than 2 years after the end of the VAT period is subject to a 12 month evidence of facts rule. The careless row is the one to watch: HMRC may be able to go back 6 years for corporation tax and the director’s income tax on the same facts where it can only go back 4 years for VAT, unless the behaviour is deliberate. Our page on how far back HMRC can go covers the extended limits.

How might a combined check play out?

Illustration only. A VAT officer visiting a small restaurant company notices that card takings in the till reports are higher than the sales in the VAT returns. The director drives an expensive car that the declared profits do not seem to fund.

The VAT officer can use Schedule 36 to obtain the till and bank records for the VAT check and assess underdeclared VAT, back 4 years if not deliberate.
The officer refers the corporation tax and director risks across. If the corporation tax enquiry window for the latest return is open, HMRC opens an enquiry; earlier years need discovery.
If the missing takings were extracted by the director, HMRC opens a linked enquiry into the director’s return with a separate notice, and an employer compliance review may follow.
Each tax produces its own assessment or amendment, appeal route and penalty, but the case may be settled together.

What should you watch for in a combined check?

Ask which taxes and which periods each officer is checking, and under what power. HMRC’s own guidance requires them to explain this.
Check whether a valid notice of enquiry has been given for each income tax or corporation tax return involved; a VAT visit is not an enquiry into the company tax return.
Work out the time limit for each tax separately rather than assuming one window applies to all.
Keep answers consistent across taxes. Information given for VAT can be used in assessing behaviour for penalties across the whole case.
If you have tax investigation insurance, check how the policy wording deals with each type of check before work starts.

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Reviewed by Christine Anderson, Broker, Solar Protect. Last reviewed 24 October 2026. Part of Accountapedia, the Solar Protect guide to UK tax and accounting. This page is general information, not personalised advice.