R&D tax in practice: the gap between theory and application

Following on from our recent blogs exploring the role of a well-reasoned “no”, and the impact that reduced confidence has had on firms stepping away from R&D tax , there’s another layer that plays directly into the confidence challenges we’ve been looking at.

The gap between understanding the rules and applying them in practice.

Understanding vs applying

Understanding the rules is one thing. Applying them – particularly when the answer isn’t obvious – is another. Advisers are often working through nuance, interpreting guidance, and making judgement calls, sometimes without a clear reference point for whether they are right.

This is not a new or ground-breaking observation – it’s widely acknowledged.

What has raised the stakes is operating in a regime that is still bedding in.

Two projects can look similar on the surface and still differ in ways that fundamentally affect whether they qualify, or how costs should be treated.

So you make a call, based on your interpretation, and you may never know whether it was the right conclusion unless that decision is tested later on downstream.

That level of uncertainty can feel uncomfortable. And, when you layer that on top of the amount of change the scheme has seen in recent years, it’s no surprise that confidence has been affected.

Why R&D tax has felt different

Accountants deal with complexity every day – interpreting legislation, responding to HMRC enquiries and handling uncertainty in other areas of tax routinely.

None of this is new, but in R&D tax, it has felt different.

The level of scrutiny, the pace of change, and the perceived risk of getting it wrong have shifted how many firms engage with it. And for some, a decision has been taken to step away entirely.

Why this matters

When firms step back from R&D tax advice delivery, it is not just a change in service offering – there is a wider knock-on effect.

It creates a gap. It reduces access to good, well-reasoned advice for the very businesses the scheme is designed to support – the claimants.

Those carrying out genuine R&D activity, often without the knowledge or confidence to navigate the rules themselves, are left with fewer trusted advisers to guide them.

And where that gap exists, other providers may step in – not always with full visibility of the client’s wider tax position or long-term interests, potentially leading to fragmentation in advice, and distance in the accountant–client relationship.

Preparing with scrutiny in mind

So, the question becomes: how do firms approach preparing robust and defensible claims with confidence?

It starts with a mindset of preparing claims on the basis that they may be reviewed by HMRC – ensuring they are well evidenced and able to stand up under scrutiny.

This looks like:

carefully reviewing evidence

documenting the reasoning behind the decisions made

ensuring any position taken can be explained and supported

Confidence, in this context, isn’t necessarily about absolute certainty. It’s about being able to justify the “why”.

Learning through doing

Experience plays a big role in building confidence. Each decision (whether it leads to a “yes” or a “no”) adds to your understanding of how the rules apply in practice.

Even highly experienced advisers will attest that this is a continual learning process.

And while an enquiry is never something actively sought, it can be one of the few opportunities for decisions to be examined in detail. Having to explain and justify a position, sometimes months or years later, can be uncomfortable, but it can also be a useful learning curve.

The role of peer discussion

Being able to test a view, challenge an assumption, or validate an approach can be invaluable.

Across the sector, it’s common for advisers, including experienced specialists, to sense-check their thinking with peers.

Whether through professional networks, communities, or internal collaboration, sharing interpretations and discussing live scenarios continually builds experience in making well-informed judgements and strengthens confidence.

For those working in smaller firms, or acting as the sole specialist, that additional perspective can be particularly helpful.

Where WhisperClaims fits into this picture

Having access to expert, reliable support can make a significant difference to the quality of the claims firms are preparing, and in turn, confidence levels.

Not to replace you as the adviser, but to provide a sounding board to sense-check a position, explore an edge case, or validate an approach before progressing further.

At WhisperClaims, this is the role our Advice Line plays, alongside our software – supporting firms as they apply the rules in practice and work through more complex or unfamiliar scenarios.

We help firms apply the rules consistently, engage with confidence and identify early on when a claim should not proceed – avoiding wasted effort, managing client expectations from the outset, and supporting a clear path to either a robust, defensible claim, or a justified decision to stand down.

Are you stepping away from R&D tax because it’s too complex…?

Or because you don’t yet have the structure to manage it with confidence?

If stepping away no longer feels like the right decision, we’re happy to show you what a more controlled, compliance-first approach looks like in practice.

Let’s talk it through