Best CIS account for MTD: side-by-side comparison

QuickBooks is the strongest functional fit, built-in CIS deduction tracking, contractor statement matching, and full MTD Income Tax support in one product. FreeAgent is the cheapest credible option if you bank with NatWest Group or open a free Mettle business account, with the same CIS feature depth. Sage Accounting also handles CIS but feels dated. Xero requires its Starter plan (£18/mo) for CIS, not the £7 Simple plan.

FreeAgent is free if you hold a business current account with NatWest, Royal Bank of Scotland, Ulster Bank or the free Mettle digital account, and it handles CIS properly. That's the only genuinely free CIS-aware MTD route. Other free MTD options (QuickFile, Pandle, HMRC's own tool) don't include built-in CIS handling, you'd track deductions manually.

Free, via FreeAgent + a free Mettle business account from NatWest Group. If that route doesn't suit, QuickBooks at around £12/mo (often discounted in the first months) is the next cheapest CIS-aware option. Xero's CIS-enabled Starter plan is £18/mo. Sage starts higher.

Not legally, MTD just requires digital records and quarterly submission, regardless of CIS. But CIS deductions are tedious to track manually, and software with built-in CIS handling will reconcile contractor statements, produce CIS suffered reports, and prevent reporting errors at year end. For active subcontractors, the £12–£19/mo for QuickBooks or FreeAgent typically pays for itself in saved bookkeeping time.

You report your gross self-employment income quarterly, the figure before any CIS deductions. The 20% (or 30%) your contractor withheld is treated as tax already paid, and HMRC reconciles it at the Final Declaration in January. Most CIS subcontractors end up with a refund because they've effectively paid tax through the year and have allowable expenses to deduct.

Yes. MTD changes how you keep records and how often you report income, not how CIS reconciliation works. Your CIS suffered total is offset against your Income Tax and NICs at Final Declaration (due 31 January after the tax year), and HMRC refunds the difference, typically within 4–8 weeks of submission.

No. The software treatment is identical for 20% and 30% deductions, only the rate changes. If you're being deducted 30% it usually means you're not registered with HMRC as a CIS subcontractor. Registering moves you to 20%, which is a meaningful cashflow win and can be done online in around a day.

No CIS-specific features are needed, contractors pay you in full and there are no deductions to track. You still need MTD-compliant software for quarterly Income Tax updates, but any HMRC-recognised tool (including the cheapest free options) is fine. You simply don't apply CIS deductions to invoices.

No. Xero's £7/mo Simple plan does not include CIS support. You need the Starter plan (£18/mo) or higher for CIS deductions, contractor matching and CIS suffered reporting. If you want a £7-ish entry point with CIS, FreeAgent via Mettle is free, and QuickBooks is often discounted in early months.

Yes, and it's the cheapest route, but you'll be tracking CIS deductions manually in your spreadsheet (gross invoice, deduction, net received as separate columns). Bridging software like 123 Sheets or My Tax Digital will submit the totals to HMRC, but doesn't understand CIS as a concept. Workable for simple cases; painful at any volume.

Not in the old once-a-year form. MTD for Income Tax replaces it with four quarterly updates plus a Final Declaration. The Final Declaration plays the role of the old Self Assessment, it's where your CIS suffered, allowable expenses and any non-CIS income come together for HMRC to calculate the final liability and refund.

Report all self-employment income together in quarterly updates, CIS doesn't get a separate stream. The CIS suffered figure is the only CIS-specific number, and it's entered at Final Declaration. Software that supports CIS will let you tag invoices as CIS or non-CIS so the deductions only apply where they should.