Managing CIS (Construction Industry Scheme) obligations can quickly become a headache, especially as your business grows and you’re juggling multiple subcontractors, monthly returns, and HMRC deadlines. Maybe it’s time for CIS Software.

If you’re still doing CIS manually (or relying on spreadsheets), you’re leaving yourself open to errors, penalties, and wasted time.

The solution? Dedicated CIS software that automates the heavy lifting.

In this guide, we’ll walk through the best CIS software options for UK construction companies, what features to look for, and which is best depending on your business size and setup.

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✅ What to Look for in CIS Software

Before we get into the tools, here are the key features your CIS software should have:

• Subcontractor verification (linked to HMRC)

• Automatic CIS deductions on labour

• Monthly CIS return filing to HMRC

• Payment & deduction statements for subcontractors

• Labour vs materials tracking

• Digital records in case of HMRC review

• Payroll and VAT integration (if needed)

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🛠️ Top CIS Software Options for Construction Companies

1. Xero (with CIS Add-On)

Best for: Small to medium-sized contractors already using Xero

Xero’s CIS feature is simple, efficient, and integrates directly with HMRC.

Key Features:

• HMRC-linked subcontractor verification

• Automatic CIS deductions on bills

• CIS return generation and submission

• Subcontractor statements

• Fully integrated with bookkeeping

💡 Tip: Combine with Xero Payroll for a full finance + CIS setup.

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2. BrightPay

Best for: Companies running payroll and CIS together

BrightPay is known for its easy-to-use payroll software, but it also handles CIS seamlessly.

Key Features:

• Run CIS alongside PAYE in one place

• Create and email deduction statements

• File monthly returns to HMRC

• Handle CIS suffered and reclaimed amounts

💡 Bonus: Desktop-based, so ideal if you prefer offline control with cloud backup.

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3. QuickBooks (UK Version)

Best for: Businesses already using QuickBooks for accounts

QuickBooks supports CIS functionality through its Advanced Payroll module or with specific settings in the contractor profile.

Key Features:

• CIS deductions on supplier payments

• Track gross, net and deducted amounts

• Attach UTRs and verification status

• Prepare CIS reports for filing

⚠️ QuickBooks doesn’t file CIS returns directly—you’ll need to do that via HMRC or a bridging tool.

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4. Eque2 Construct for Sage

Best for: Larger contractors using Sage 50 or Sage 200

Eque2 provides an industry-specific construction management add-on for Sage software.

Key Features:

• End-to-end construction finance management

• CIS processing and subcontractor management

• Labour/materials costing

• Project tracking, contract variations, and CVR

💡 Ideal for firms needing cost control + CIS in one system.

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5. SubbieHub (Specialist Tool)

Best for: Contractors managing 50+ subcontractors

SubbieHub is a CIS-focused tool built specifically for construction businesses.

Key Features:

• Manage subcontractor onboarding

• Automated CIS verifications and returns

• Secure digital subcontractor portal

• Integration with Xero and QuickBooks

📲 A good option if your main system lacks depth for CIS, and you need a bolt-on tool.

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6. Payroll Manager by Moneysoft

Best for: Budget-conscious firms with straightforward needs

Simple, reliable desktop-based CIS and payroll software for smaller firms.

Key Features:

• Handles CIS, PAYE and pensions

• Files directly to HMRC

• Generates CIS300 returns and subcontractor statements

• Low-cost, one-off licence

💷 Good value for small contractors, but lacks cloud or mobile access.

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🤔 So, What’s the Best CIS Software for You?

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✅ Benefits of Using CIS Software

• Saves hours of admin time

• Reduces risk of HMRC penalties

• Keeps records tidy for audits

• Improves cash flow visibility

• Helps you stay on top of deadlines

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👷‍♂️ Need Help Choosing or Setting Up CIS Software?

At Thomas Emlyn Ltd, we help construction companies:

• Choose the right CIS software based on size and workflow

• Set it up correctly with subcontractor verification, returns and statements

• Handle monthly CIS admin as part of our Virtual Finance Office (VFO) service

📞 Book a free discovery call and let’s take CIS off your to-do list – for good.

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📌 Final Thoughts

CIS doesn’t have to be a monthly burden. With the right software, you can automate 90% of the process and stay fully HMRC compliant with less stress.

Whether you’re a one-man band or running multiple teams across sites, there’s a CIS solution that fits your business.