HMRC R&D Compliance Check Defence
Written and reviewed by the R&D Tax Accountants editorial team. Last reviewed 8 August 2026.
HMRC checked 9,700 R&D claims in 2023 to 2024, covering 17% of them, and recovered £441 million. If a letter has arrived, this is the service you need, and it is work we take on for claims we did not prepare.
Of the compliance checks HMRC settled that year, 89% were resolved by agreement with the claimant. A check is not a verdict. What determines the outcome is the quality of the evidence and the discipline of the response.
What a Compliance Check Involves
HMRC has 12 months from the date the claim was submitted to open a check, and it opens some after the credit has already been paid so that compliant claimants are not held up. A payment received is not a claim agreed, and a repayment demand can follow.
The questions usually go to the same places: which scientific or technological uncertainty the project faced, why a competent professional could not readily resolve it, how the staff time apportionment was arrived at, and whether external labour was restricted correctly. Those are the four areas worth preparing for before the deadline on the letter.
HMRC's second Mandatory Random Enquiry Programme, looking at 2021 to 2022 claims, found around half of SME claims non-compliant in part or in full and 30% non-compliant in full. That is the base rate a compliance officer is working from, and it is why a thin answer is read as a confirmation rather than a clarification.
Where Enquiry Responses Go Wrong
The most common failure is answering with more of the original narrative. If the first description of the work did not identify the uncertainty in the terms the legislation uses, restating it at greater length does not help, and it uses up the goodwill available in the correspondence.
The second is volume. Sending everything is not the same as sending what was asked for, and a large unstructured bundle invites more questions rather than fewer. The third is answering in commercial language, which reads to HMRC as an absence of a technical answer.
The fourth is missing the routes out. Where progress stalls, alternative dispute resolution is available during a check as well as at the end of one, with HMRC saying within 30 days whether it is suitable and participants committing to a meeting within 90 days of acceptance. It does not affect the right to appeal or to ask for a statutory review.
How We Handle a Check
We read what was actually filed before responding to anything: the narrative as submitted, the costing and what it was built on, and the correspondence to date. Sometimes the honest conclusion is that part of the claim was overstated, and knowing that early changes the strategy from defence to correction.
Where the claim is sound, the response is built around the statutory test, evidenced from contemporaneous records, and structured so each HMRC question has an answer against it. Where part of it is not sound, there is a disclosure route for overclaimed relief that cannot be corrected by amending the return, with HMRC responding within 30 calendar days, and penalties are typically reduced where a disclosure is unprompted.
That second path is not a defeat. A company that corrects a bad claim on its own initiative is in a materially better position than one that defends it to a conclusion and loses. Guidance on both HMRC's compliance approach and the disclosure route is published by HMRC.
Fees for Enquiry Work
Enquiry work is scoped to the check and the correspondence rather than to preparing a claim, and the fee is agreed in writing before it starts. We will tell you at the outset what we think the realistic range of outcomes is, including where we think the claim is weak.
If you have not been checked and want to reduce the chance of it, a review before filing is a cheaper piece of work than a defence afterwards.