CIS Management Software for UK Contractors

The Problem

CIS goes wrong when UTRs live in spreadsheets, verification replies sit in email, and the deduction rate lives in the bookkeeper’s head. Apply the wrong rate and you either short-pay a subbie, under-deduct and carry the liability yourself, or send a CIS300 that does not match what you actually paid out.

What Changes

Onboard each subbie with their UTR and NI, check their CIS status with HMRC, record the verification number and deduction rate against their record, and have every payment pull the right 0%, 20% or 30% automatically — with a full history of every change.

The HMRC verification number and result saved against the subbie0%, 20% or 30% applied to every payment automaticallyUTRs and NI numbers stored securely — never shown in plain textFull history of every recorded result and every rate change

How It Works

From a brand-new subbie to the right deduction on their next payment — keep CIS consistent and easy to evidence, with each HMRC check recorded once against the subbie instead of lost in an inbox.

1
Onboard the subbie with their UTR and NI
Capture legal name, trading name, CIS self-employment status, 10-digit UTR and NI number through the onboarding flow. UTRs and NI numbers are stored securely — only opened inside the CIS workflow.
A subcontractor record (Eastbridge Drainage Solutions, approved, insurance expiring) — the CIS & Compliance panel shows a Net 20% deduction rate, the HMRC verification result recorded on 21/04/2026 with its verification number, the UTR, SVN and NI number and three workers, beside contact details, the active mobile app invite, day and hourly rates and a health declaration panel.
2
Check them with HMRC and record the result
Check the subbie with HMRC online or by phone, then record the result on their record — matched status (gross, net or unmatched), deduction rate and HMRC verification number all land on the subcontractor profile. Site Samurai does not contact HMRC for you.
The CIS screen where you record the result of each HMRC check — every subcontractor with their CIS status (Net 20%, Gross 0% or Higher Rate 30%), the deduction rate every bill uses, the last-verified date and HMRC verification number, and a Record result or Update result button on each row.
3
Apply the right deduction rate
The rate HMRC returned — 0% for Gross Payment Status, 20% for verified net, or 30% for a subbie HMRC can’t match — sits on the subcontractor record. If you record a new result with a different rate, it flows through to any payments you haven’t posted or paid yet so the deduction stays in line with what HMRC says.
4
Pay with the deduction worked out for you
When you raise a weekly payment for a subbie, we apply the current rate to the labour element and show you the CIS deduction alongside the net payable. No more scribbling 80/70/100 maths on the back of a payment schedule.
The Subcontractor Whereabouts approval screen for Week 41, 05/10/2026 to 11/10/2026 — the week’s subcontractor submissions reviewed and approved in one place, with 5 subcontractors over 16 days carrying £8,040 gross before CIS, £1,464 CIS deductions and £6,576 net payable, and three Northfield Bypass Upgrade submissions awaiting approval, each at its own CIS rate (Higher 30%, Gross 0% and Standard 20%) with gross, CIS and net per subbie.
5
Issue the payment and deduction statement
Every payment shows gross, deduction and net paid per subbie — the line-level detail you need to reconcile against the CIS300 monthly return you send HMRC (via HMRC online services or your accounting package) and to give each subbie their monthly payment and deduction statement.
6
Record the new result when something changes
If a subbie’s CIS status changes — for example, they get Gross Payment Status — check them with HMRC again and record the new result. The new rate is saved with a fresh date, your accounts inbox gets an email so accounts know before the next payment run, and the before-and-after is kept in the record.

Features That Move The Needle

Built for high-stakes construction workflows: deadlines, compliance, and audit trails.

HMRC result recorded on every subbie

The HMRC verification number, tax treatment and deduction rate are saved against the subcontractor — with the last-verified date, so you always know how fresh the check is.

UTR and NI stored securely

UTRs and NI numbers are stored securely and only opened inside the CIS workflow. They never appear in plain text in logs or exports — which is what GDPR and ICO guidance for personal tax data expects.

A new rate flows through to unpaid work

When a recorded result changes the rate, payments you haven’t posted or paid yet are updated too — so the deduction can’t drift away from what the subbie’s recorded status says it should be.

Every subbie’s CIS status in one list

See each subbie’s CIS status, deduction rate, HMRC verification number and last-verified date in one searchable list — handy before tax year-end, after a bulk re-onboarding, or when you inherit a supply chain list from an acquired project.

A record of every recorded result

Every result you record, and the rate change it causes, is kept with who recorded it and the rate it replaced. When HMRC asks why a subbie was paid at 20%, the answer is in the record.

Email alert when a result is recorded

When someone records a new result — say a subbie moves from 30% to 20%, or from 20% to gross — your accounts inbox gets an email, so accounts and commercial know before the next payment run goes out.

Approved subbie list

Reuse verified subbies across jobs without re-running onboarding. The approved list sits alongside the CIS status, so you see at a glance who’s ready to mobilise and at what rate.

Unlimited users with the right access

Commercial, accounts, site and payroll each see the CIS data they need. Unlimited users on every plan — you don’t pay per seat as the team grows.

UK CIS built in

Aligned with the CIS framework HMRC actually enforces

Site Samurai’s CIS workflow is built around the UK statutory and regulatory framework that governs subcontractor tax: Finance Act 2004 Chapter 3, the Income Tax (Construction Industry Scheme) Regulations 2005, and HMRC’s operational guidance in CIS340. We track and apply; we do not replace HMRC.

Finance Act 2004 — Chapter 3 (Construction Industry Scheme)

The statutory basis of CIS. It defines who is a contractor, who is a subcontractor, and the deduction regime that applies to payments for construction operations. Site Samurai’s subcontractor model, CIS record and deduction rates are modelled against this scheme.

Finance Act 2004 Part 3 Chapter 3 on legislation.gov.uk

Income Tax (Construction Industry Scheme) Regulations 2005 (SI 2005/2045)

The operational regulations under Finance Act 2004. They set the verification rules, the monthly return obligations, the 19th-of-month reporting deadline, and the record-keeping requirements. The audit log, encrypted UTR/NI storage, and last-verified date tracking are designed against these regs.

SI 2005/2045 on legislation.gov.uk

HMRC CIS340 — guide for contractors and subcontractors

HMRC’s operational guidance on running CIS: verification flow, the 30% higher rate for unverified subcontractors, the 20% standard rate for verified net, 0% for Gross Payment Status holders, and the monthly return mechanics. Site Samurai’s deduction rates and email alerts follow this guidance.

CIS340 on GOV.UK

Why not just use HMRC online, Sage/Xero, or a spreadsheet?

Most UK SME contractors start with one of three approaches before their CIS process breaks. Here is what goes wrong and where Site Samurai fits.

HMRC online CIS service

Free — but manual, one subcontractor at a time
No single list of every subcontractor’s status alongside your payments
Results sit in HMRC until someone keys them into your payment run
No audit log linking verification to the subbie record in your system
Re-keying UTRs is where mistakes (and 30% mis-deductions) creep in

Sage / Xero CIS modules

Accounting-first — CIS is a bolt-on, not a subcontractor lifecycle tool
Good for the CIS300 return; weaker for onboarding, verification workflow, and document trail
Deduction rate lives in the ledger, not alongside insurance and qualification data
No cascade to a live payment whereabouts workflow on site
Typically no self-serve subcontractor onboarding portal

Spreadsheet + HMRC portal

UTRs stored in plain text in shared drives — GDPR / ICO red flag
Verification status drifts — nobody remembers when a subbie was last checked
No audit log when someone quietly changes a deduction rate from 30% to 20%
Re-verification after a CIS status change relies on someone remembering
Falls apart the moment the person running it is off sick

Site Samurai

HMRC result recorded on every subbie — status, rate and verification number
0% / 20% / 30% deduction rate stored against the subbie record
UTRs and NI numbers stored securely — only opened inside the CIS workflow
A record of every recorded result and every rate change
A new rate flows through to payments you haven’t posted or paid yet

Site Samurai isn’t an accounting package and it doesn’t file your CIS300 — we’re upfront about that. What it does do is record each subbie’s HMRC verification result, hold UTRs and NI numbers securely, apply the right 0%, 20% or 30% deduction to payments, and give you a record that stands up when HMRC asks how a rate was set.

Free CIS templates — use them today, software or not

Three CIS-ready templates you can use on your next subbie onboarding or monthly reconciliation. No signup. Want the whole workflow joined up — the HMRC result recorded once, secure storage, and the right rate flowing through to every payment? Start a trial or book 15 minutes with Rich.

CIS Subcontractor Onboarding Form

Collect legal and trading name, UTR, NI, CIS self-employment status, and contact details. Designed around the Finance Act 2004 Chapter 3 subcontractor record so nothing is missed before first verification.

PDF

CIS Verification Checklist

Step-by-step checklist for verifying a subcontractor under HMRC CIS340: what to hold, what to ask, how to record the verification number, and when to re-verify.

PDF

Approved Subcontractor List

Spreadsheet template for tracking your approved supply chain with CIS status, deduction rate (0/20/30), verification number, and last-verified date. Use it before upgrading to the live, encrypted workflow.

XLSX

Seen enough?

Start a 14-day free trial — you won’t be charged until it ends, or book 15 minutes with Rich (the founder) to walk through your exact workflow.

Not ready? Grab the free templates instead →

Why It Works

Every subbie carries their CIS result: HMRC verification number, tax treatment, deduction rate and last-verified date. UTRs and NI numbers are stored securely, every recorded result is kept in the record, and when a rate changes it flows through to any payments you haven’t posted or paid yet — so the deduction always matches the subbie’s recorded status.

Site Samurai — built for UK SME contractors

Built around Finance Act 2004 Chapter 3 and the CIS Regulations 2005

Unlimited

Users on every plan

20% / 30% / 0%

Deduction rates handled

Encrypted

UTR + NI storage

Who It’s For

If you're the ops manager chasing HMRC replies and verification numbers across inboxes every time a new subbie lands on site
If you're the SME director whose name is on the CIS liability — and you need to sleep at night knowing verifications are current
If you're in accounts on the 14th of the month staring down a CIS300 deadline and chasing deduction-rate evidence from three systems
If you co-ordinate subcontractors and your current 'verified list' is a spreadsheet that nobody trusts after 90 days
If you run a specialist trades or civils firm where 80% of labour is subcontracted and CIS compliance is non-negotiable
If you're a main contractor with a supply chain of 50+ subbies and need audit-grade evidence before the next HMRC letter arrives

Already using Site Samurai? Jump to the module features and workflows your team needs.

FAQ

Frequently Asked Questions

Common questions teams ask before they book a demo.

CIS is the HMRC scheme governing tax deductions on payments from contractors to subcontractors in UK construction. It is set out in Finance Act 2004 Chapter 3 and the Income Tax (Construction Industry Scheme) Regulations 2005 (SI 2005/2045), with operational guidance in HMRC CIS340. Contractors must verify each subcontractor before paying them, apply the correct deduction rate to the labour element, and report monthly to HMRC.

Site Samurai does not contact HMRC. Once a subbie is onboarded with their UTR and (where needed) NI number, you check them with HMRC online or by phone and record the result against the subcontractor: matched status, deduction rate, HMRC verification number and last-verified date. We then apply that rate to their payments.

HMRC sets the rate based on the subbie’s CIS registration and history. 0% (gross) means they hold Gross Payment Status — you pay the full amount and they settle their own tax. 20% is the standard rate for a verified net subcontractor. 30% is the higher rate for a subbie HMRC can’t match against their records — usually because they’re not registered for CIS. Site Samurai applies the rate you record from HMRC.

Per CIS340, a subbie who hasn’t been verified — or whose details HMRC can’t match — has to be paid at the 30% higher rate. The subcontractor profile flags unverified status so your payment run doesn’t accidentally pay an unverified subbie at 20%. Check them with HMRC and record the result so the right rate is saved before the next payment cycle.

No — this matters and we won’t overclaim. Site Samurai records the result of your HMRC check, stores UTR and NI securely, applies the right deduction on payments, and keeps the record of it all. You still send the CIS300 monthly return through HMRC online services or your accounting package (Sage, Xero, FreeAgent and the like). We give you the clean line-level data to reconcile against the return — we don’t file it for you.

The CIS tax month runs 6th to 5th. Your CIS300 monthly return and any CIS tax payment to HMRC are due by the 19th of the month after the tax month (or the 22nd if you pay electronically). Miss the 19th and HMRC charges penalties — even on a nil return — so the payment data inside Site Samurai is built to let you pull the monthly totals well before the deadline.

To check a subbie with HMRC you need their UTR (the 10-digit Unique Taxpayer Reference) and their legal name. For sole traders, we also hold the NI number because it’s part of the identity HMRC uses. Both are stored securely on the subcontractor’s profile and only opened inside the CIS workflow.

UTRs and NI numbers are stored securely against the subcontractor record. They’re only opened briefly inside the CIS workflow. They’re never written to logs in plain text, and they don’t appear in CSV exports or error reports. That matches ICO guidance for personal tax data.

Every result you record is kept with who recorded it, when, the matched status and the rate before and after; the latest verification number and CIS status stay on the subcontractor’s record. Your accounts inbox gets an email each time, and when the rate changes the new rate flows through to any payments you haven’t posted or paid yet — so the deduction can’t quietly drift from what HMRC said.

Yes. Book a free 15-minute demo with Rich, the founder — he built Site Samurai for his own groundworks company, which runs CIS end-to-end. He’ll walk you through recording the HMRC result, the deduction on a live payment, secure UTR and NI storage, and how the record lines up against your CIS300 — so you can see exactly what the product does (and what it doesn’t) before starting a trial.