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, verify their CIS tax treatment with HMRC, store the verification number and deduction rate against the record, and have every payment pull the right 0%, 20% or 30% automatically — with a full history of every change.

HMRC verification with the verification number 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 verification 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, without re-typing UTRs into HMRC’s portal every time a new lad lands on site.

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 when we send them to HMRC for verification.
A subcontractor record open on the CIS and Compliance panel — tax status shown as Verified at 20%, HMRC verification number, UTR and NI fields, insurance expiry, agreed rates and contact details all on one screen.
2
Verify them with HMRC
Run a CIS verification with HMRC from the subbie’s record. Test mode returns realistic responses so you can try the flow end-to-end; the live HMRC connection is rolling out. Either way, the reply — tax treatment (gross, net or unregistered), deduction rate and HMRC verification number — lands straight on the subcontractor record.
The CIS Verification screen listing every subcontractor with their CIS status (Net 20%, Not Registered 30%, Not Verified), deduction rate, last-verified date, HMRC verification number, and a Re-verify 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 the rate changes on a re-verification, it flows through to any payments you haven’t paid out 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 weekly subcontractor payment run — week dates and a countdown to the deadline, totals for subcontractors, days, gross, CIS deductions and net payable across the board, and the list of subbies still missing an entry with an Add entry button on each.
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
Re-verify when something changes
If a subbie’s CIS status changes — for example, they get Gross Payment Status — run verification again. The new rate is saved with a fresh date, your ops team 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 verification 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 when we send them to HMRC. 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 verification changes the rate, payments you haven’t paid out yet are updated too — so the deduction can’t drift away from what the subbie’s verified status says it should be.

Verify your whole supply chain at once

Run verification across every subbie from one screen — 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 verification

Every verification — whether it goes through, fails, or changes the rate — is kept with who ran it and what HMRC said. When HMRC asks why a subbie was paid at 20%, the answer is in the record.

Email alert when the rate changes

If a re-verification moves a subbie from 30% to 20%, or from 20% to gross, your ops team 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, verification flow, 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 cascade and ops-team 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 bulk verification workflow across your supply chain
Verification results sit in HMRC — they do not flow 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 CIS verification on every subbie — test mode ready, live connection rolling out
0% / 20% / 30% deduction rate stored against the subbie record
UTRs and NI numbers stored securely — only opened when we send them to HMRC
A record of every verification and every rate change
A new rate flows through to payments you haven’t paid out 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 run the subcontractor verification with HMRC, 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 — HMRC verification, 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 with no card required, 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 verification result: HMRC verification number, tax treatment, deduction rate and last-verified date. UTRs and NI numbers are stored securely, every verification is kept in the record, and when a rate changes it flows through to any payments you haven’t paid out yet — so the deduction always matches the subbie’s verified 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 re-typing UTRs into HMRC's portal one by one 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.

Once a subbie is onboarded with their UTR and (where needed) NI number, you run verification from their record. Test mode returns realistic responses so you can try the flow end-to-end; the live HMRC connection is rolling out. Either way, the reply is saved against the subcontractor: tax treatment, deduction rate, HMRC verification number and last-verified date.

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 whichever rate HMRC returned.

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%. Run verification to get the right rate saved before the next payment cycle.

No — this matters and we won’t overclaim. Site Samurai handles subcontractor verification, secure UTR and NI storage, applying the right deduction on payments, and keeping 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.

HMRC verification needs the subbie’s 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 when we send them to HMRC.

UTRs and NI numbers are stored securely against the subcontractor record. They’re only opened briefly when we send them to HMRC for verification. 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 verification is kept in the record with who ran it, when, and what HMRC returned (the verification number and the deduction rate). When the rate changes, your ops team gets an email, and the new rate flows through to any payments you haven’t paid out 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 verification, 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.