Xero
Every plan lists “Automate subcontractor CIS calculations and reports”. “Submit contractor CIS returns” is £5 a month more, and its cheapest plan, Ignite, allows 20 invoices and 10 bills a month (its pricing page, 5 October 2026). On Xero’s own ideas forum, “CIS deduction after retention - subcontractor invoices”, posted on 3 May 2023, had 47 votes and the status Submitted when we checked on 4 October 2026.
What it means for you: a contractor pays £276 a year before VAT to file from Ignite, and a month with more than 20 invoices needs a dearer plan.
In Stoneledger: both sides of CIS in the one £8 plan, with no monthly limits, and retention tracked from the invoice, with the CIS worked at the rate in force when it is paid.
QuickBooks
Every plan lists “Calculate and submit CIS”, and payroll is an add-on on every plan (its pricing page, 5 October 2026).
What it means for you: its list stops at the contractor’s calculation and return. Nothing on it checks the statements a contractor sends you, or flags a deduction taken at the wrong rate.
In Stoneledger: every statement you receive is reconciled against what you were paid, a deduction at the wrong rate is flagged, and your refund is tracked all year.
Sage
Its first plan with CIS is Accounting Standard, at £43 a month before VAT, so a business in CIS moves up from Sage’s starting plan to get it (its pricing page, 5 October 2026).
What it means for you: £516 a year before VAT just to have CIS - more than ten years of Stoneledger’s yearly plan.
In Stoneledger: CIS is in the £8 plan from the start, for the subcontractor and the contractor.
FreeAgent
Free with some business bank accounts: HMRC lists it as “FreeAgent for free with Mettle, NatWest & RBS” (4 October 2026). Its help centre says the monthly CIS300 return cannot be filed from FreeAgent: you prepare it there and file it on HMRC’s own online service (5 October 2026).
What it means for you: a contractor still files every return by hand, twelve times a year, with a penalty for each one that is late.
In Stoneledger: the CIS300 is built from your books to HMRC’s own specification, and the penalty clock runs on screen until it has gone. Sending it from Stoneledger comes once HMRC grants access.