Trade software that handles CIS: Tradify, Fergus, Xero, EstiMate

"Handles CIS" can mean four different things, and software websites rarely tell you which one they mean.

1. Working out the deduction on an invoice. As a subbie, that's what the contractor will take off your labour. As a contractor, it's what you take off your subbies.
2. Keeping a register of what's been deducted, so the figures are there at month end and year end.
3. Verifying subcontractors and sending them statements.
4. Filing the contractor's monthly return, the CIS300, to HMRC.

Reverse-charge VAT usually turns up on the same invoices, so we've covered that too; our reverse charge guide explains the rules.

Short answer: if you want the monthly return filed from your software, QuickBooks does it at no extra cost and Xero does it with a CIS add-on. EstiMate, YourTradebase, Powered Now, FreeAgent and Zoho Invoice work out deductions on the invoice; Powered Now and FreeAgent also help prepare the return, but you still submit it through HMRC. Tradify's own help centre says you need Xero or Sage connected to create a CIS invoice, and we couldn't find CIS features in Fergus.

Who does what

"Not found" means we searched the vendor's site and help centre in October 2026 and found nothing. It isn't proof the feature is missing, so ask the vendor.

Prices checked October 2026: Tradify £34 to £44 per user a month, VAT basis not stated; Fergus from £39 per user (some Fergus pages show £35), VAT basis not stated; Xero £18 to £70 a month ex VAT, plus the CIS add-on; FreeAgent £19 to £33 ex VAT; Powered Now £28 to £40 ex VAT; YourTradebase £29 ex VAT; EstiMate £15.99 per business, one office login, which is what you pay. QuickBooks' UK prices conflicted between sources in our research, so check its pricing page.

Tradify: CIS goes through your accounts package

Tradify is clear about this in its own help centre. It "does not have any native Reverse VAT / CIS tax options", and "you can not create a CIS invoice in Tradify unless you are connected with Xero or Sage Business Cloud" (Tradify help). With QuickBooks there's no CIS integration; the workaround is editing the invoice in QuickBooks (Tradify help). On Xero, reverse-charge invoices have to be tax-exclusive or they won't sync.

Those help articles are a couple of years old, so check they're still current. If they are, a Tradify user on CIS is really paying for two apps. We go through the rest of the comparison in Tradify alternative for UK builders.

Fergus: we couldn't find it

Fergus has a clear blog explainer on what CIS is and who pays it (Fergus Tradehub). But we couldn't find a CIS deduction or reverse-charge feature in its help centre, and its invoicing settings article says to manage tax adjustments in your accounting package (invoicing settings). Fergus syncs with Xero, MYOB and QuickBooks, which is where its help centre points you for tax. If CIS matters to you, test it on the 14-day trial. Our Tradify vs Fergus vs EstiMate post puts all three side by side.

Xero: deductions built in, filing for £5 more

Xero works out CIS deductions automatically, and subcontractors get a "Suffered CIS" report (Xero CIS guide). Filing CIS returns, verifying subcontractors and emailing statements is a CIS add-on at £5 a month ex VAT on all plans (Xero CIS returns). One Xero page says contractors need Ignite or above, and the pages conflict a little, so check the add-on on the live page. It also has reverse-charge VAT rates with the invoice wording, and MTD VAT returns from Ignite.

Between them, Xero and QuickBooks are the strongest options here if you want the return filed from software, and if your accountant already works in Xero, that counts for a lot. More in Xero for builders.

EstiMate: CIS on the job, figures ready for filing

EstiMate takes CIS deductions where the job lives and keeps a CIS register, and reverse-charge invoices carry the required wording. The Accounts tab adds a P&L for any period, a VAT return helper, aged debtors and year-end exports for your accountant, plus cost exports in Xero and QuickBooks formats. That's a file export, not a live sync. See construction accounting software.

What it doesn't do: file CIS returns or VAT returns to HMRC. It prepares the figures and the register. The submission is done by you, your accountant or software that files. If you're a contractor with a few subbies and an accountant who files for you, that split works well. If you file your own monthly return and want it done in one click, QuickBooks or Xero with the add-on will suit you better. Our CIS guide explains the rules.

The others worth knowing

• QuickBooks: Intuit says contractor CIS needs Simple Start or above, and its Sole Trader plan is for subcontractors only. CIS returns are e-filed to HMRC "at no extra cost" (QuickBooks UK CIS). Reverse-charge codes at 20% and 5% flow to the VAT return, though a community reply says the invoice wording has to be added by hand. Read QuickBooks for builders.
• Powered Now: switch CIS on, flag the customer or supplier, and it estimates the deduction on sales invoices. There's a CIS 300 report for contractors, marked "Pro only" in its help centre (check which plans that covers), but filing is still done on HMRC's portal (Powered Now CIS). See EstiMate vs Powered Now.
• FreeAgent: CIS for subcontractors and contractors. The contractor monthly return exports as PDF or CSV, but FreeAgent says "it's not currently possible to file CIS300 returns using FreeAgent", so you file through HMRC's online service (FreeAgent CIS300). Read FreeAgent for builders.
• YourTradebase: deductions at 0%, 20% or 30% from the labour total, with a default per customer. Its Xero sync includes CIS; its one-way QuickBooks sync doesn't (YourTradebase help). More in YourTradebase vs EstiMate.
• Zoho Invoice: enter your UTR and NI number, tick "Covered by CIS?" on the invoice and the deduction is worked out. It isn't supported on expenses (Zoho CIS help). See Zoho Invoice for builders.

We couldn't find CIS features in ServiceM8 or Jobber either.

Which setup suits you

• Subbie invoicing a main contractor: you need the deduction and reverse-charge wording right on the invoice. EstiMate, YourTradebase, Powered Now, FreeAgent and Zoho Invoice all do the deduction.
• Contractor paying subbies monthly: you need the register and the return. QuickBooks files it; Xero files it with the add-on. EstiMate keeps the register, and you or your accountant file.
• Both at once: pick one app for the job side and one place where returns get filed, and stop typing the same numbers twice.

If CIS is eating your evenings, start free and set up your next job in EstiMate.