The opening letter
The check announces itself in writing, typically identifying the return and claim, asking a first round of questions and setting a response date. HMRC’s own factsheet frames the purpose neutrally: checking that the right tax is paid and reliefs correctly claimed. For R&D specifically, its compliance guidelines say plainly that HMRC may ask for anything reasonably needed to evidence your claim: project records, the basis of apportionments, prototypes and test results, and the competent professional’s reasoning.
Three early decisions matter. Decide who owns the response internally: the named senior contact from the AIF should expect to be central. Decide whether your adviser is engaged for the enquiry. And set a realistic response timetable you then actually meet. If a deadline is impossible, ask for more time before it passes, not after.
The middle: questions, evidence, sometimes a conversation
Expect iterations. Answers generate follow-ups; strong answers generate fewer. The pattern that serves companies well:
- Answer the question asked, precisely, then stop. Volunteered essays open new fronts.
- Lead with contemporaneous evidence. A test log from the time beats a beautifully written recollection. HMRC’s guidance explicitly warns that without records you may struggle to evidence the claim.
- Put the competent professional forward for the technical points, prepared, and let finance handle the numbers. Mixed voices blur both.
- Stay civil and punctual. The factsheet is explicit that cooperation can shorten the check and reduce any penalty. Obstruction has the opposite effects, and formal information powers sit behind polite requests.
The end: three outcomes
- Accepted. The check closes with no change. It happens, more often to claims built for scrutiny.
- Adjusted. Parts hold, parts do not; the claim is recalculated, with interest on anything repayable and possible penalties depending on behaviour.
- Rejected. HMRC concludes the claim fails, issues decision notices, and the disagreement machinery begins: statutory review by an uninvolved officer, appeal to the independent First-tier Tribunal, or Alternative Dispute Resolution alongside. None of these removes the others. That path has its own page: if your claim is rejected.
Penalties, in honest proportion
Where an inaccuracy is found, penalties are behaviour-based percentages of the lost tax. Broadly: nothing where reasonable care was taken; up to 30% for carelessness; 20% to 70% for deliberate understatement; and up to 100% where concealed. Reductions follow the quality and promptness of disclosure, and unprompted disclosure of a careless error can reduce to nil. Which is the practical argument for finding problems yourself first: amending a past claim covers the correction routes, including HMRC’s dedicated disclosure facility.
Frequently asked questions
How long does an R&D enquiry take?
From a few months for a clean claim with fast responses to well over a year where facts are contested. The variables you control are response speed and evidence quality; slow, partial answers are the single biggest self-inflicted delay.
Will HMRC visit or interview us?
Most R&D checks run by correspondence, sometimes with a call between your competent professional and HMRC's. Meetings happen in larger or harder cases. A well-prepared technical lead is an asset in any format.
Should we just accept HMRC's view to end it?
Not reflexively. Caseworkers are sometimes right and sometimes wrong, and conceding a sound claim sets your baseline for every future year. Equally, defending the indefensible burns credibility and racks up interest. The decision should follow the evidence, coldly.
Can HMRC reopen a claim it already paid?
Yes. Payment is processing, not approval, and checks regularly open after money has moved. Never treat the credit as final until the enquiry window has closed.