What Does a CIS Accountant Do? A Complete Guide for Contractors and Subcontractors

A CIS accountant helps contractors and subcontractors manage Construction Industry Scheme deductions, tax returns, bookkeeping, payroll and HMRC compliance. If you work in construction, the right accountant should do more than file numbers at year end. They should help you understand what has been deducted, what you can claim, what records to keep, and when a problem needs fixing before HMRC gets involved.

At Brickbooks and Payroll, we work exclusively with trades and construction businesses who need accountancy support that fits the way they actually operate. CIS can look simple from the outside, but the day to day reality is often messy: changing sites, mixed labour, delayed paperwork, materials, mileage, retentions, subcontractor payments and tight cash flow.

Why CIS Accounting Needs Construction Specific Attention

The Construction Industry Scheme affects how contractors pay subcontractors and how subcontractors receive income. Under HMRC’s CIS guidance, contractors deduct money from a subcontractor’s payments and pass it to HMRC. Those deductions then count towards the subcontractor’s tax and National Insurance bill.

That sounds straightforward until the records do not match.

A common issue is that subcontractors know money has been deducted, but they do not have the right statements to prove it. Another is that contractors pay people as subcontractors without checking the setup properly. CIS sits close to payroll, bookkeeping and tax, so a small admin mistake can spread quickly.

A general accountant may still be able to file a return. A CIS accountant should understand the construction-specific questions behind the return, such as whether labour has been treated correctly, whether materials have been separated, and whether the business has enough records to defend the figures.

What Does a CIS Accountant Do Day to Day?

A CIS accountant deals with the practical accounting work linked to the Construction Industry Scheme. That can include checking CIS deductions, preparing tax returns, reconciling monthly statements, supporting payroll, reviewing bookkeeping records, and helping contractors meet HMRC deadlines.

We often see CIS problems come from ordinary admin gaps rather than deliberate mistakes. Someone forgets to collect a deduction statement. A payment gets split between labour and materials in the wrong way. A subcontractor changes status. The earlier these issues are picked up, the easier they are to correct.

Suggested read: What Is CIS? The Construction Industry Scheme Explained

CIS Accountant Support for Subcontractors

If you are a subcontractor, your CIS accountant should help you understand what your deductions mean and how they affect your tax return. CIS deductions are not an extra tax. They are advance payments towards your final tax bill.

Good support usually includes:

• Getting you registered properly. If you are not registered for CIS, contractors must deduct 30% from your labour instead of 20%. Your registration also needs to match your legal name, not your trading name, or contractors may not be able to verify you
• Making sure materials are not taxed. Deductions should only come off your labour. If your invoices do not show materials separately, tax can be taken from the full amount
• Recording CIS deductions from contractor statements and checking them against bank payments
• Preparing and filing your Self Assessment tax return, including every CIS deduction and allowable expense
• Filing early when a refund is due. The tax year ends on 5 April, and you do not have to wait until January. Filing soon after means your refund can arrive months sooner
• Helping you get gross payment status when you qualify, so contractors pay you in full with no deductions, and keeping your filing on time so you do not lose it at HMRC’s annual review

Record keeping matters. HMRC may ask for evidence of income, deductions, mileage, tools, materials, insurance, phone costs or other business expenses. If your paperwork is scattered across WhatsApp, emails and glovebox receipts, the tax return becomes harder than it needs to be.

Our advice is simple: keep CIS statements, invoices, receipts and bank records together throughout the year.

Suggested read: When Should You Register as a CIS Subcontractor?

CIS Accountant Support for Contractors

If you are a contractor paying subcontractors, CIS responsibilities sit with you. You need to register for CIS, verify subcontractors with HMRC, deduct the correct amount from labour payments, provide payment and deduction statements, and submit monthly CIS returns.

This is where delays and assumptions can get expensive. HMRC will tell you to use 20% for registered subcontractors, 30% for unregistered subcontractors, or 0% if the subcontractor has gross payment status. If labour and materials are not separated clearly, with evidence for materials the subcontractor paid for directly, the deduction may be wrong, and HMRC can come to you for the difference.

A CIS accountant can build a routine that keeps the process clean:

• verify subcontractors before payment
• separate labour and materials clearly
• issue deduction statements by the 19th of each month
• file monthly CIS returns by the 19th of each month
• file nil returns in months when no subcontractors were paid, which mainstream contractors have had to do again since 6 April 2026
• reconcile payments against bookkeeping records
• spot missing information before deadlines

Late CIS returns bring automatic penalties, starting at £100 per return and rising the longer they are outstanding. Having someone own the deadline takes that risk off your plate.

Suggested read: When Do You Need to Register as a CIS Contractor?

CIS Accountant Support for Limited Companies

Limited companies that have CIS deducted from their income do not claim it back on a tax return. Instead, the deductions are set off each month against the PAYE, National Insurance and CIS the company owes HMRC, through payroll.

This is one of the most commonly missed areas. If the set-off is not claimed properly, the company pays HMRC more than it needs to every single month. A CIS accountant makes sure the set-off is claimed through payroll, and that any amount left over at the end of the tax year is refunded or set against Corporation Tax.

The Difference Between CIS, Payroll and Normal Bookkeeping

CIS is not the same as payroll, even though both involve payments and HMRC reporting. Payroll usually applies to employees. CIS applies to many subcontractor payments in construction.

Bookkeeping records what has happened in the business: money in, money out, invoices, receipts, expenses and bank activity. CIS then adds another layer because deductions must be tracked and reported properly.

The mistake is treating CIS as a year-end tax problem. It is monthly, practical and record-led. If the bookkeeping is weak, CIS becomes harder. If CIS is wrong, the tax return becomes less reliable.

This is why construction businesses often need accounting support that connects the dots. A builder might need bookkeeping, VAT support, payroll, CIS returns and year-end accounts. Looking at each part separately can miss the pattern. If you need help with wages, payslips and regular reporting too, it makes sense to review your bookkeeping and payroll services at the same time.

Common CIS Mistakes to Avoid

The biggest CIS mistakes are usually basic, but they are still painful.

One is failing to verify subcontractors before paying them. Another is applying deductions to the wrong part of the invoice. Under HMRC’s deduction rules, deductions are calculated after taking off costs such as VAT, plant hire and materials the subcontractor paid for directly, so the breakdown matters. Contractors may also need receipts or other evidence to support those material costs.

Subcontractors have their own traps. Some assume CIS deductions mean they do not need to file a tax return. Others forget to claim allowable expenses because they have not kept receipts. A few expect a refund, then find their records do not support the figures.

There is also the cash flow problem. CIS deductions reduce the money subcontractors receive during the year. If you do not track them properly, it is hard to know whether your tax position is healthy or whether you are relying on a refund that may not arrive as expected.

Do I Need a General Accountant or a CIS Accountant?

Many contractors and subcontractors start with a general accountant, especially if their accounts are simple. That may be enough if you only have occasional construction income and your CIS records are already clean.

A CIS accountant is usually the better fit when CIS affects your cash flow, monthly reporting, subcontractor payments or tax refund position. The difference is not just the job title. It is the type of questions they know to ask.

Situation	General accountant	CIS accountant
You need a basic Self Assessment tax return	May be suitable	Suitable, especially if CIS deductions are involved
You are missing CIS deduction statements	May record what you provide	Should help identify gaps and reconcile deductions
You pay subcontractors regularly	May need extra context	Better suited to verification, monthly returns and deduction statements
You need help separating labour and materials	May offer general bookkeeping support	Should understand how CIS deductions apply to labour payments
You expect a CIS tax refund	May file the return	Should check deductions, expenses and evidence before the claim
Your limited company has CIS deducted	May miss the payroll set-off	Should claim the set-off every month through payroll
You run a construction business with payroll and CIS	May handle each area separately	Should connect CIS, payroll, bookkeeping and year-end accounts

 

If CIS is a small part of your business, a general accountant may be enough. If CIS is part of how you get paid, how you pay others, or how your tax position is worked out, specialist CIS support is usually worth it.

How to Choose the Right CIS Accountant

A good CIS accountant should be comfortable asking practical questions. How do you invoice? Do you supply materials? Are you paying subcontractors or being paid as one? Are you VAT registered? Do you use software? Do you have deduction statements for each contractor?

You do not need someone who makes tax sound clever. You need someone who can make the process clear and keep you compliant. Look for:

• Construction experience. CIS, the VAT domestic reverse charge and subcontractor employment status all interact, and a specialist will spot problems a generalist will not
• Professional regulation. Check the firm is supervised by a recognised professional body such as the AAT, ACCA or ICAEW
• Monthly and year-end support in one place, so bookkeeping, payroll, CIS returns and accounts do not fall between the gaps
• Clear, fixed pricing, so you know what you pay each month and what is included
• Easy switching. Changing accountants should not be your job. A good firm contacts your old accountant and handles the handover for you

At Brickbooks and Payroll, we are down-to-earth and personable, but we also believe fit matters. If we are not the right accountant for your needs, we will help point you towards someone who is.

Frequently Asked Questions

Do I need a CIS accountant if I am a subcontractor?

You do not legally need a specialist CIS accountant, but it can make your tax return much easier. CIS deductions, expenses and records need to be handled correctly if you want an accurate tax bill or refund.

Can a CIS accountant help me get a tax refund?

Yes, if your CIS deductions are higher than your final tax liability and your records support the claim. An accountant cannot guarantee a refund, but they can make sure deductions and allowable expenses are recorded properly, and file soon after 5 April so the refund arrives sooner.

Do I need a CIS accountant if I run a limited company?

If your company has CIS deducted, it is well worth it. The monthly payroll set-off is one of the easiest places for a company to overpay HMRC.

What records should I keep for CIS?

Keep CIS deduction statements, invoices, receipts, bank statements, mileage records and evidence for business expenses. The cleaner your records are, the easier it is to prepare your return and answer HMRC questions.

Is CIS the same as being self-employed?

No. CIS is a tax deduction scheme used in the construction industry. Many CIS subcontractors are self-employed, but the scheme itself is about how payments are reported and deducted.

Can I switch accountants part way through the year?

Yes. You can switch at any point, and your new accountant will request what they need from your previous one.

Need Help With CIS Accounting?

CIS is easier to manage when the records are clean, the monthly routine is clear, and someone is checking the details before they become a tax-year headache. If you are guessing at deductions, chasing missing statements or unsure what HMRC expects, it is time to get proper support.

Brickbooks and Payroll works exclusively with trades and construction businesses across Bedfordshire and nationally. Our team are CIS accountants for subcontractors, contractors and limited companies, handling CIS returns, payroll, VAT, bookkeeping, tax returns and year-end accounts, and we take care of the switch from your current accountant.

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Prefer to talk it through? Call 01234 413751 or email info@brickbooksandpayroll.com.

This article is general guidance based on HMRC’s published CIS guidance at the time of writing. Your own position may differ, so speak to an accountant before acting on it.