How Accountants Help with HMRC Enquiries and Audits

Most people panic when they receive a brown envelope from HMRC. The wording is formal, the tone feels intimidating and the implications appear serious even when the enquiry is routine. I always tell clients that an HMRC enquiry does not automatically mean something is wrong. In many cases HMRC are simply checking figures, comparing data or asking for clarity. The real problem only appears when the business owner tries to handle it alone.

This is where an accountant becomes essential. We know what HMRC are looking for, how they review records and what evidence they expect to see. We speak their language so you do not have to. We remove emotion from the process and deal with it logically and professionally which is exactly what HMRC want.

Why HMRC Open Enquiries

HMRC begin enquiries for many reasons. The most common triggers include:

• Figures that do not match HMRC records
• VAT returns that look inconsistent
• Large changes in profit from one year to another
• A Director’s Loan Account that appears overdrawn
• Missing information
• Random selection for routine checks
• Incorrect PAYE or CIS submissions
• Suspicious expense claims
• Data pulled from banks, employers or online platforms

The point is that enquiries are normal. They happen every day across Bedford. What matters is how you deal with them.

How accountants take control of the process

When we help a client with an HMRC enquiry the first thing we do is take responsibility for the communication. Most clients feel anxious and do not know how to reply. HMRC letters are worded in a way that can easily be misinterpreted. Our role is to make the process calm and structured.

Here is exactly how we handle it.

Step 1: We contact HMRC on your behalf

We take over all communication so you no longer have to deal with HMRC directly. We request more time if needed, clarify the scope of the enquiry and set the expectations clearly. This alone reduces your stress because you do not need to worry about saying the wrong thing or missing a deadline.

Step 2: We review your records and check for issues

Before responding we go through your bookkeeping, returns and supporting documents to see:

• Whether the submissions were correct
• Whether any figures look inconsistent
• Whether any expenses need rechecking
• Whether your VAT codes are accurate
• Whether your Director’s Loan Account is correct
• Whether any adjustments are required

If there is an issue we fix it. If everything is correct we prepare evidence to show HMRC clearly.

Step 3: We prepare a professional response

HMRC want information that is clear, complete and factual. We prepare a full response pack that includes:

• A cover letter explaining the position
• A breakdown of the numbers
• Supporting records
• Explanations written in HMRC friendly terms

The goal is to answer every question directly and remove any uncertainty so HMRC can close the enquiry quickly.

Step 4: We negotiate where appropriate

Sometimes HMRC make incorrect assumptions or ask for adjustments that are not valid. This is where experience matters. We challenge the points that are wrong and support the points that are correct. HMRC respect accountants who understand the rules and provide proper evidence. This often reduces penalties or removes them entirely.

Step 5: We handle follow up questions

Enquiries sometimes involve multiple rounds of questions. We deal with every follow up request until the case is closed. This keeps the process tidy and removes any pressure from you. Our priority is always to resolve the enquiry with the least impact on your business.

Step 6: We prevent future enquiries

Once the enquiry is finished we speak with you about the cause. We adjust your systems, improve your bookkeeping and strengthen your processes so the same issue does not happen again. This is where long term value comes from because one improvement today can prevent several enquiries in the future.

The types of HMRC enquiries accountants deal with

We regularly support clients with:

• VAT inspections and compliance checks
• Corporation tax enquiries
• CIS reviews
• Payroll and RTI investigations
• Self Assessment enquiries
• Director’s Loan Account reviews
• Evidence checks for expenses
• Random audits
• Penalty disputes

Each type requires a different approach but the principle is always the same. Provide clear evidence, correct errors honestly and keep the process organised.

Why you should not handle HMRC enquiries yourself

Clients often try to deal with HMRC before contacting an accountant. By the time they come to us they have already sent long explanations, partial information or contradictory details because they were trying to be helpful. This makes the enquiry worse because HMRC now have more questions.

Trying to handle everything alone can lead to:

• Incorrect explanations
• Misinterpretation of HMRC’s request
• Missed deadlines
• Higher penalties
• Unnecessary stress
• Damage to your tax record
• Longer enquiry times

In my opinion the moment you receive an HMRC letter you should contact an accountant before responding. One simple call can save you weeks of stress.

Common mistakes we see clients make before they come to us

• Sending too much information
• Sending not enough information
• Guessing instead of checking
• Blaming software
• Sending emotional or defensive responses
• Ignoring the letter completely
• Providing figures that do not match the return
• Trying to fix the bookkeeping after the response

These mistakes make enquiries harder for both you and HMRC. Having the accountant handle everything keeps it clean, logical and professional.

How Towerstone supports clients during HMRC enquiries

At Towerstone we work hand in hand with our clients during the entire enquiry process. We take over the communication, prepare the technical responses, organise the records and negotiate with HMRC directly. Our clients never deal with HMRC alone.

We do not offer weekend or in person evening appointments but we do speak with clients during early evenings when needed because we understand enquiries feel urgent and stressful. Our focus is always to remove that pressure from you and resolve the issue as smoothly as possible.

Clients often tell us that having us speak to HMRC on their behalf is the biggest relief because they no longer have to worry about saying the wrong thing or misunderstanding the request.

The Bottom Line for Bedford Business Owners

Yes accountants can help with HMRC enquiries and audits. In fact a good accountant can make the entire process straightforward, stress free and far less intimidating. HMRC enquiries are not something you should face alone. With the right support you can protect your business, reduce penalties and resolve issues quickly without panic.