Last verified: October 2026
It is the 17th of the month, and the office manager at a groundworks contractor is verifying two new subcontractors with HMRC, working out deductions from invoices that lump labour and materials together, and trying to get the CIS300 in before the 19th.
CIS software does different jobs depending on which side of the scheme you are on. Contractors verify subcontractors, deduct 20% or 30% from the labour part of each payment, file a monthly return and send deduction statements. Subcontractors record what was deducted, claim it back and, from April 2026, many keep digital records for Making Tax Digital. This guide compares the main CIS software for both sides, with October 2026 prices, the plan each tool needs for CIS, and what none of them do for you.
Where Planyard Fits
Planyard does not file CIS returns, so it is not ranked below. It sits in front of your accounting software and handles the part that decides whether the deduction is right: subcontractor applications, the certified amount, retention, and the labour and materials split, which is set once on the subcontract order. The approved bill then posts to Xero, QuickBooks or Sage, which applies the deduction and files the return.
CIS Software Compared
Prices are per month excluding VAT, as published in October 2026, for the cheapest plan that includes what is listed.
| Software | For | Contractor returns | Statements to subcontractors | CIS cost per month | Best for |
| Xero | Both | £5 add-on | Yes, with add-on | £18 + £5 | Firms whose accountant works in Xero |
| QuickBooks Online | Both | Included from Simple Start | Yes | £16 | Lowest price with filing included |
| Sage Accounting | Both | Included from Standard | Yes | £43 | Small firms that want Sage in the cloud |
| Sage 50 + CIS module | Contractors | Paid module | Yes | £115 + £11 | Firms with an in-house accounts team |
| FreeAgent | Both | Included | Yes | £19 to £33, or free with some banks | Sole traders and micro contractors |
| CIS Manager | Contractors | Included | Yes | £20 for 20 subcontractors, then £1 each | CIS only, alongside any accounts package |
| Moneysoft Payroll Manager | Contractors | Included | Yes | £95 to £285 a year | Desktop payroll and CIS together |
| BrightCIS | Contractors, bureaus | Included | Yes | Quote | Accountants and payroll bureaus |
| HMRC CIS online | Contractors | Yes | No | Free | One or two subcontractors |
What CIS Software Needs to Do
If you pay subcontractors
- Verify each new subcontractor with HMRC to get their deduction rate: 0% for gross payment status, 20% if registered, 30% if not
- Deduct only from the labour part of the payment, never from materials, plant hire or VAT
- File the CIS300 return by the 19th of every month. From April 2026, a month with no payments needs a nil return or advance notice to HMRC. How to file the monthly return walks through it
- Send payment and deduction statements to each subcontractor within 14 days of the end of the tax month
- Apply domestic reverse charge VAT where the subcontractor is VAT registered and you are not the end user
If you are a subcontractor
You need to record each deduction against the matching invoice, keep the statements, and claim the deductions back: through Self Assessment as a sole trader, or through your EPS as a limited company. From 6 April 2026, sole traders with qualifying income over £50,000 must keep digital records and send quarterly updates under MTD for Income Tax, and the threshold drops to £30,000 in April 2027.
None of the tools below decides how much of an invoice is labour. Someone sets that split on every bill, and a wrong split is the most common reason a deduction, and so the return, is wrong. How CIS works covers the rules in full.
Best CIS Software for Contractors
1. Xero – Best for Growing Firms with a Xero Accountant
Xero calculates CIS on every plan and records deductions suffered for subcontractors at no extra cost. To verify subcontractors and file contractor returns, you add the “Submit contractor CIS returns” option for £5 a month. Bills coded to a CIS subcontractor have the deduction worked out from the labour lines, and the monthly return and statements come from the same data.
Most UK accountants work in Xero, so this is usually the path of least resistance.
Best for: Contractors growing past a handful of subcontractors whose accountant already uses Xero.
Watch out for: Contractor filing is an add-on, so the real price is £5 above the headline plan.
Pricing: Ignite £18, Grow £39, Comprehensive £55, Ultimate £70, plus £5 for contractor returns.
"We had to get our accountant on board and interface it with Xero, so invoices hit the right job number. Now an invoice gets uploaded in Planyard, I sign it off, and it drops into my Xero payment schedule in three or four weeks – it’s perfect."
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2. QuickBooks Online – Best Value with Filing Included
QuickBooks calculates CIS for contractors and subcontractors and e-files to HMRC at no extra cost. It also handles domestic reverse charge VAT and, with QuickBooks Payroll, runs PAYE for employees alongside CIS for subcontractors.
Sole Trader Plus (£10) is aimed at subcontractors; Intuit points contractors who file CIS returns to the business plans from Simple Start up.
Best for: Small contractors who want the lowest monthly cost with filing built in.
Watch out for: Fewer UK accountants use it than Xero, so check yours is happy to work in it.
Pricing: Simple Start £16, Essentials £38, Plus £56, Advanced £123. Payroll is extra.
3. Sage Accounting or Sage 50 – Best for Firms with a Finance Function
Sage Accounting, the cloud product, includes CIS, MTD and domestic reverse charge from the Standard plan. Sage 50, the desktop product, sells CIS as a separate module. Both verify subcontractors, file returns and produce statements, and Sage payroll covers employees.
Choose by how your accounts team works: Sage 50 for an in-house team that has used it for years, Sage Accounting for a smaller firm that wants Sage without the desktop install.
Best for: Contractors with an accounts team, or an accountant, already on Sage.
Watch out for: The entry plans do not include CIS: Sage Accounting Start (£20) and Sage 50 without the module both leave it out.
Pricing: Sage Accounting Standard £43. Sage 50 Standard £115 or Professional £234, plus £11 for the CIS module.
4. FreeAgent – Best for Sole Traders and Micro Contractors
FreeAgent has handled CIS for subcontractors for years and added contractor CIS in July 2025, so a small firm can pay its own subcontractors and file the return in the same account. Deductions suffered feed straight into Self Assessment.
It is free with a NatWest, RBS, Ulster Bank or Mettle business account, which makes it hard to beat on price for a one-person business that occasionally subcontracts.
Best for: Sole traders and very small limited companies who are both subcontractors and occasional contractors.
Watch out for: Built for micro businesses. It is not the tool for a contractor with dozens of subcontract packages.
Pricing: Sole trader £19, partnership £24, limited company £33. Free with selected business bank accounts.
5. CIS Manager – Best CIS-Only Tool
CIS Manager (cismanager.com) does CIS and nothing else. You record invoices and payments, it calculates deductions, files the monthly return and sends statements to subcontractors. Verifications are free, and subcontractors never pay to register or share their details.
It suits a contractor who is happy with their accounts package but wants CIS out of a spreadsheet.
Best for: Contractors who want CIS handled separately from their accounts, and accountants running CIS for several clients.
Watch out for: It is another system to keep in step with your ledger, so payments are recorded twice unless you import them.
Pricing: £20 a month for up to 20 subcontractors paid, then £1 for each extra one. Charged only on accepted returns. Free for subcontractors.
Payroll Tools with CIS
If you employ staff as well as paying subcontractors, a payroll tool that includes CIS keeps both in one place. This is the “CIS payroll software” most accountants mean.
Moneysoft Payroll Manager is Windows desktop software that runs PAYE payroll and CIS, including verification, returns and statements. An annual licence costs £95 for up to 20 employees and subcontractors at one employer, £190 for up to 100, and £285 for up to 250. It does not run on a Mac.
BrightCIS, from the company behind BrightPay, is a standalone CIS service for verification, returns, statements and subcontractor payments, priced per subcontractor on a quote. BrightPay moved CIS out of its payroll product into BrightCIS and retired its desktop app after 5 April 2026, so former desktop users now run payroll in BrightPay Cloud.
HMRC’s free CIS online service lets you verify subcontractors and file the monthly return. It does not calculate deductions or produce statements, so it works for a contractor with one or two regular subcontractors and not many more.
"The best part is that I only have to do things once instead of twice; it’s great to have everything in a single, efficient system."
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Get the labour split right before the bill reaches your accounts
Set the split once on the subcontract order and let Xero, QuickBooks or Sage apply the deduction. 14-day free trial, no credit card.
Best MTD Software for CIS Subcontractors
Subcontractors need less: somewhere to record income, expenses and deductions suffered, and MTD-compatible submission once your income is over the threshold. MTD and CIS in 2026 explains what changes.
- FreeAgent (£19, or free with NatWest, RBS, Ulster Bank or Mettle): the most complete option for a sole trader, with deductions feeding Self Assessment
- Clear Books Sole Trader Free (£0): HMRC recognised for MTD for Income Tax and set up for CIS subcontractors, with paid plans from £5 if you want bank feeds and invoicing
- QuickBooks Sole Trader Plus (£10): CIS for subcontractors and MTD for Income Tax, with receipt capture and mileage
- Xero Ignite (£18): records deductions suffered on every plan and is MTD ready, a sensible choice if your accountant works in Xero
If you also take on your own subcontractors, pick a tool that does both sides. FreeAgent, QuickBooks and Xero all do; Clear Books needs its Medium business plan for contractor returns.
How to Choose
One or two subcontractors, no payroll: HMRC’s free service, or FreeAgent if you also want your books in one place.
Up to about 20 subcontractors: QuickBooks Simple Start on price, Xero with the add-on if that is what your accountant uses.
Employees and subcontractors: Sage with payroll, QuickBooks with payroll, or Moneysoft if you prefer desktop software.
Several live projects with subcontract packages: the CIS software is the easy part. The hard part is checking applications, holding retention and agreeing the labour split before the bill is posted. That is where Planyard sits, in front of Xero, QuickBooks or Sage.
"All of the financial data and invoices are sent automatically to Xero and emailed to my bookkeeper, who then has all the information she needs to record it correctly in our accounts. It’s sort of job done, as simple as that."
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Next Step
Pick the CIS software your accountant works in, then make sure every bill reaches it with the right subcontractor and the labour split already set. Planyard does that part, and does not file returns itself. See how it works with Xero, QuickBooks and Sage.
CIS returns built from bills that are right the first time
Planyard sets the labour and materials split on the order, tracks applications and retention, and posts approved bills to Xero, QuickBooks or Sage. 14-day free trial.