Construction Payroll & PAYE Management:
Payroll That Keeps CIS and PAYE Apart, and Correct
Construction payroll rarely stays simple for long, employed staff on PAYE, subcontractors under CIS, and people moving between the two as contracts start and finish. We run your payroll, keep CIS and PAYE reconciled against each other, and flag the working arrangements that HMRC would question before HMRC does
- Cash Flow Specialists
- Construction Payroll Specialists
£3.1m+
CIS Recovered
100 %
HMRC & MTD Ready
50+
Five-Star Reviews
Construction
Tax EXPERTS
Fixed Fee
No hidden charges
HMRC Compliance
Who We Are
Accountants who reconcile CIS and PAYE, not just process a pay run
Most construction payroll problems don’t show up in the pay run itself, they show up when CIS deductions and PAYE figures stop agreeing with each other and with the year end accounts. Our accountants for construction run your payroll each period and reconcile the two systems together, so a subcontractor wrongly treated as PAYE, or staff quietly paid on invoice, gets caught early rather than at a HMRC review.
PAYE payroll processed each period, with real time submissions to HMRC
CIS and PAYE figures reconciled monthly, so the two agree with each other and your accounts
Getting Starters, Leavers, & Holiday Pay Right
A workforce that moves between sites shouldn’t mean records that fall behind
Labour that comes on for a big contract, goes back to invoicing when it finishes, then returns months later is normal in construction, but it’s exactly where starters and leavers pile up and holiday pay gets calculated on the wrong basis. We process starters and leavers properly across every site, and work out holiday pay correctly for people whose earnings vary week to week, which is one of the most common sources of underpayment claims in the trade.
100%
CIS Compliance Rate
Protecting You From Employment Status Risk
A CIS registration settles nothing about whether someone is really self employed
Registering a subcontractor under CIS decides what comes off their payment, it says nothing about whether HMRC would treat them as employed once it looks at how the work is actually controlled. Where a subcontractor works your hours, uses your tools, and cannot send a substitute in their place, the exposure sits with you as the main contractor, and it grows the longer the arrangement continues unreviewed.
We review employment status on arrangements that look wrong and give you a written view on each one, while assessing auto enrolment every period so pension duties on a changing workforce don’t get missed.
Employment status reviewed on arrangements that look wrong, with a written view on each one
Auto enrolment assessed every period, so pension duties on a changing workforce don’t get missed
Common Pain Points
What Goes Wrong With Construction Payroll
Most construction payroll problems come from a small set of recurring, fixable causes.
CIS and PAYE Mixed Up Between Systems
Subcontractor payments run through PAYE by mistake, or staff paid on invoice because it was easier at the time, and the two returns stop agreeing with each other.
Employment Status Left Unreviewed
A long standing subcontractor working your hours with your tools can be an employee in substance regardless of what the CIS registration says.
Auto Enrolment Missed on a Changing Workforce
Pension duties follow every employee you take on, and a workforce that changes every few months is where assessments get missed and warning letters start arriving.
Holiday Pay Calculated on the Wrong Basis
Construction workers whose pay varies week to week need holiday pay worked out correctly for how they’re actually paid, not a flat average.
CIS Deductions Never Reconciled Against HMRC
Deductions taken off your invoices through the year have to match what HMRC has recorded, and unreconciled gaps sit unclaimed indefinitely.
Free Consultation
Let’s talk about your construction accounting challenges
Book a 30-minute call with our specialist accountant for construction business. We’ll look at how your business is set up and flag quick wins you can act on straight away.
- CIS and VAT reverse charge handled correctly
- Deep expertise in contractor, subcontractor tax rules
- Forward-looking advice, not just year-end filing
- Transparent fixed fees, no surprises
Our Services
Complete Construction Payroll and CIS Management
From the pay run through to employment status risk, we manage the full payroll picture as your construction accountant.
PAYE Payroll Processing
We run your payroll each period, with payslips, reports, and real time submissions to HMRC.
CIS and PAYE Reconciliation
We keep the two systems properly apart and reconciled, so your CIS return, PAYE return, and accounts all agree.
Employment Status Reviews
We review arrangements that look wrong and give you a written view on where you stand before HMRC asks.
Auto Enrolment Management
We assess pension duties every period and handle contributions as your workforce changes.
Starters, Leavers & Holiday Pay
We process workforce changes across every site and calculate holiday pay correctly for variable earners.
CIS Suffered Reconciliation
We reconcile deductions taken from your invoices against your HMRC record and chase gaps.
Client Stories
Real feedback from real construction businesses
Over 60 verified five-star reviews from subcontractors, contractors and developers across the UK.
★★★★★
“I’d been under-claiming CIS repayments for two years without realising it. They found and recovered £14,000 within weeks of taking us on. Nobody had ever explained the scheme to me this clearly before.”
★★★★★
“We had no real idea which contracts were making money until they built us a proper job-costing system. Now we price the next tender based on actual data, not guesswork.”
★★★★★
“Every site brings its own VAT and SDLT questions, and they have never once been slow to answer. Switching from our old firm was the easiest financial decision we have made in years.”
FAQS
Commonly Asked Questions about Construction Payroll and PAYE
Does registering a subcontractor for CIS make them self employed?
How much retention can I expect to have tied up at any time?
Typically 5% of contract value, split between practical completion and the end of the defects period, though this varies by contract terms.
Can I do anything about clients who consistently pay late?
Yes, stronger payment terms, deposit requirements, and active credit control can significantly reduce how long cash stays outstanding.
Who is liable if HMRC disagrees with how we've treated a worker?
The contractor, in practice; HMRC pursues the business that made the payments, and any correction can run back over the full period the arrangement has been in place.
Can CIS and PAYE payroll be run together?
Yes, and it’s the sensible approach, since reconciling the two together is exactly where errors between them surface early.
Does using an agency or umbrella company solve the status question?
Not by itself, it changes who employs the worker and brings its own checks, so the underlying contracts still need reviewing.
Why choose Construction Tax Accountants for payroll and PAYE?
We reconcile CIS and PAYE as one connected system rather than two separate processes, and we raise employment status risk directly instead of leaving it for HMRC to find first.
Still have questions?
Our construction accountants are ready to answer any questions about your specific tax situation with no obligation for an initial conversation.
- Mon–Fri, 9am–5:30pm