Best accounting software for construction and CIS

The right accounting software for construction depends on which side of the Construction Industry Scheme (CIS) you are on. Contractors need software that verifies subcontractors and files the monthly CIS300 return to HMRC; subcontractors mainly need to track deductions taken from their invoices. This page lists five products alphabetically, using each provider’s own pages checked on 6 November 2026, without ranking them.

Quick comparison of CIS software

Entry prices for CIS features run from free for subcontractors to £34 a month for contractor returns. Prices exclude VAT.

The “HMRC CIS300 list” column refers to HMRC’s CIS commercial software suppliers page, updated 27 November 2025. HMRC says listed products have proved they can file a valid CIS300, and that it does not endorse any product.

What CIS software needs to do

CIS software should handle the tasks HMRC sets out in What you must do as a CIS contractor:

• Verify subcontractors before you pay them, unless they appeared on a return in the current or last 2 tax years
• Apply the right deduction: 20% for registered, 30% for unregistered, 0% for gross payment status
• Deduct on labour only, not on materials
• File the monthly return by the 19th after the tax month ends on the 5th
• File a nil return or make an inactivity request in months with no payments
• Issue payment and deduction statements to each subcontractor
• Handle the domestic reverse charge for VAT on construction services

GOV.UK says you need commercial software to verify more than 50 subcontractors. A return filed even one day late costs £100.

The five products

Clear Books. Its pricing page lists “CIS reporting and submissions, for construction” on the Medium plan (£34 a month) and Large plan (£44 a month). The Small plan (£16) does not list CIS. All three sole trader plans, including Sole Trader Free, say they work for CIS subcontractors. Clear Books is on HMRC’s CIS300 list.

FreeAgent. FreeAgent’s CIS page says contractors can store each subcontractor’s deduction rate, UTR and verification number, view CIS300 data, and export it as PDF or CSV “to streamline your external filing”. It does not say returns are filed to HMRC from FreeAgent. For subcontractors, it tracks deductions and offsets them against payroll for limited companies. Plans run from £19 a month for sole traders to £33 for limited companies, with 50% off the first six months.

QuickBooks. The QuickBooks CIS page says it calculates contractor and subcontractor deductions and e-files to HMRC “at no extra cost”. The pricing page lists “Calculate and submit CIS” on Sole Trader Plus, Simple Start, Essentials, Plus and Advanced. Prices showed “Loading live prices” when we checked, so we cannot quote one. QuickBooks is not on HMRC’s CIS300 list.

Sage Accounting. Sage’s CIS set-up guide, last modified 12 August 2026, shows how to switch on CIS as a contractor, subcontractor or both, entering your UTR and PAYE references. Sage’s pricing pages blocked our check, so we have not printed a price or the plans that include CIS. HMRC’s list names Sage 50cloud Accounts and Sage 200cloud, not Sage Accounting.

Xero. Xero’s CIS page says CIS calculations are on Ignite and above. A £5 a month add-on covers verifying subcontractors, filing monthly returns to HMRC and bulk emailing statements. Plans cost £18 (Ignite), £39 (Grow), £55 (Comprehensive) and £70 (Ultimate) a month, with 90% off the first six months for new customers. The CIS suffered report helps subcontractors. Xero Business Edition is on HMRC’s list.

Construction-specific software

HMRC’s list also includes construction products such as BuildSmart, COINS, Easy Build, Sledgehammer CIS and Mercurius Construct CIS. These suit firms that also need job costing, valuations or retentions. We have not checked their prices.

Which applies to you?

• If you are a subcontractor only, you need deduction tracking, not CIS300 filing. Clear Books Sole Trader Free, FreeAgent, QuickBooks and Xero all cover this.
• If you are a contractor paying a few subcontractors, look for direct CIS300 filing: Clear Books Medium, Xero with the CIS add-on, or QuickBooks.
• If you are happy to file on HMRC’s online service, FreeAgent’s export may be enough.
• If you pay more than 50 subcontractors, you must verify through commercial software.
• If you need job costing and retentions, compare the construction-specific products.
• If you are a sole trader subcontractor, check MTD for Income Tax support too; see MTD for CIS subcontractors.

What to do now

1. Decide whether you are a contractor, a subcontractor, or both. Our guides to CIS for contractors and CIS for subcontractors explain each role.
2. Check the product on HMRC’s CIS software list if you want to file CIS300 from the software.
3. Test subcontractor verification and the reverse charge VAT codes in the free trial.
4. Confirm the price on the provider’s page on the day you sign up.
5. Read our construction accounting guide for retentions and job costing.

Frequently asked questions

Which accounting software can file CIS returns to HMRC?

HMRC’s recognised list, updated 27 November 2025, includes Clear Books, Xero Business Edition and Sage 50cloud Accounts. QuickBooks also says it e-files CIS to HMRC, though it is not on that list.

Does Xero charge extra for CIS?

Yes, for contractors. CIS calculations are on every plan, but verifying subcontractors and filing returns costs £5 a month plus VAT.

Can FreeAgent file CIS300 returns?

FreeAgent’s pages say it prepares CIS300 data and exports it as PDF or CSV for external filing. They do not say it files the return to HMRC.

Is there free CIS software for subcontractors?

Yes. Clear Books’ Sole Trader Free plan says it works for CIS subcontractors, with no monthly fee when we checked on 6 November 2026.

Do I need software to verify subcontractors?

Only if you verify more than 50. GOV.UK says commercial software is needed above that number; below it you can use HMRC’s own online service.