HMRC Compliance & Enquiries

HMRC compliance, enquiries and risk

R&D relief is now a compliance regime with a tax incentive attached, and pretending otherwise is how companies get hurt. This pillar collects the whole risk side in one place. It covers why the scrutiny exists, how checks actually run, how claims are defended, corrected and sometimes honestly abandoned, and the records that make all of it boring.

Written and reviewed by the InnoClaim team, a firm of Chartered Tax Advisers. Last reviewed 8 July 2026.

Why the scrutiny exists

HMRC measured, published and acted. That is the short version. Random-enquiry results put error and fraud at 17.6% of relief for 2021-22, concentrated in the old SME scheme. The response was staffing, screening paperwork, sector campaigns and, in the end, scheme reform. The numbers, and what they mean for honest claimants, are on the crackdown, in numbers. The selection patterns they produced are on what triggers an enquiry.

Before you claim: the honesty checks

The cheapest compliance work happens before filing, and three pages carry it. When you do not qualify collects the plain no’s most marketing omits. Red flags in your own claim is a graded fifteen-point self-audit. Common errors that sink claims organises the same failures by family and fix. Between them they encode the position this firm is built on. The willingness to find problems, including the problem of no claim at all, is what makes the rest of the advice worth having.

If HMRC looks: checks, defence, disputes

A compliance check has a shape: opening letter, evidence, conclusion. Knowing the shape removes most of the fear, and what happens in an enquiry walks through it. Holding a sound claim through a check is a method, not a mood; the method is on how to defend a claim. Where HMRC decides against you, the routes are independent and they stack. Review, mediation and tribunal are on if your claim is rejected.

Putting things right

Corrections run in both directions inside the two-year window. Beyond it, overclaims have a dedicated disclosure facility, with penalty ranges built to reward whoever moves first. Both are on amending a past claim.

Certainty in advance

For small first-time claimants, and for four named hard questions, HMRC will look before you leap. Advance assurance covers it, including the targeted pilot introduced in May 2026.

The foundation: records

Every page above lands on the same floor: what was written down at the time. HMRC’s expectations are specific and modest. Meeting them costs almost nothing when built into normal work, and record-keeping for R&D claims shows how.

Sources
  1. HMRC, Approach to Research and Development tax reliefs 2023 to 2024, gov.uk
  2. HMRC, GfC3: Help to see if your work qualifies as R&D for tax purposes, gov.uk
  3. HMRC, About compliance checks (CC/FS1a), gov.uk

Frequently asked questions

How likely is our claim to be checked?

HMRC reported checking about 17% of claims in 2023-24, with selection part random and part risk-based. Plan on the assumption that any claim can be examined, because that assumption produces better claims.

What single thing most reduces compliance risk?

A claim built to be checked: an honest technical narrative with its boundary drawn, costs that reconcile with evidence behind the apportionments, and the process deadlines hit. No relationship, reputation or adviser substitutes for that.

Are enquiries hostile?

Mostly procedural. HMRC's factsheets frame checks as verifying the right reliefs, and cooperation is explicitly rewarded in both speed and penalties. Hostility, where it appears, usually arrives after evasiveness.

What if we conclude our own claim was wrong?

Correct it, quickly and on your own initiative: amendment inside the window, HMRC's disclosure facility beyond it. The penalty rules are engineered to make the unprompted correction the cheap one.

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