The best MTD software for CIS subcontractors

If you work in construction as a self-employed subcontractor, you're probably paid under the Construction Industry Scheme (CIS). That adds a layer to your bookkeeping, because what lands in your bank is often less than what you invoiced. Making Tax Digital doesn't change CIS, but it does mean you'll need software that keeps your records straight and sends quarterly updates to HMRC.

HMRC treats CIS subcontractors who are sole traders like any other sole trader for MTD. Whether you need it depends on your gross turnover (HMRC MTD FAQs). We compared the main options for CIS support and price, and checked every price in October 2026.

What are CIS deductions, in plain English?

Under CIS, the contractor who hires you may take a deduction from your payments and pass it to HMRC on your behalf. Think of it as money set aside towards your tax bill before you get paid. Your contractor should give you a statement showing what was deducted each month.

At the end of the year, those deductions are taken into account when your tax is worked out. You might owe more, or you might be due money back. Exactly how that works for you depends on your situation, so we won't go into the detail here.

The best MTD software for CIS subcontractors at a glance

Prices exclude VAT unless stated and were checked on each provider's website in October 2026. Introductory offers change often, so always confirm the live price. App ratings are from the UK App Store and Google Play in October 2026.

The best CIS software for subcontractors in detail

Xero supports CIS and handles MTD for Income Tax. The Simple plan is £7 a month ex VAT, and you can move up to plans with VAT returns and payroll without changing software. That matters if you might take on your own labour one day and become a contractor yourself. Most UK accountants who work with trades know Xero well. Read our Xero review.

Watch out for: Simple doesn't do VAT returns. If you're VAT registered, you'll need a higher plan. Check which plan includes the CIS features you need. Full price: Simple £7, Ignite £18, Grow £39, Comprehensive £55, Ultimate £70 a month, all ex VAT. Promotional discounts often run for new customers.

QuickBooks covers subcontractors on its Sole Trader plan, with full CIS on higher plans. Sole Trader Plus costs £10 a month ex VAT. Providers say you can snap receipts for materials and track mileage with GPS, which suits people moving between sites. Its apps are rated 4.7 on iOS and 4.6 on Android. Read our QuickBooks review.

Watch out for: Sole Trader Plus doesn't do VAT returns. Intro offers change often, so check the live price.

Clear Books supports CIS and has a free Sole Trader plan with MTD for Income Tax included. If your records are simple and you're happy to type transactions in, you can stay compliant without paying. The £5 a month plan adds bank feeds (your bank transactions flow in automatically).

Watch out for: the app is rated just 2.9 on iOS, so it's better on a laptop than on site. VAT returns need Sole Trader Plus at £15 a month.

Sage's CIS support sits on Sage Accounting Standard, which costs £43 a month ex VAT. That plan also includes VAT returns. It's a solid choice if you're a busier, VAT-registered subcontractor, or if your accountant prefers Sage.

Watch out for: the cheap Sage Sole Trader plans shown in the card above don't list CIS, so you'd need to pay for Accounting Standard. That's much more than Xero or QuickBooks for a simple setup.

Zoho Books has a generous free plan with MTD for Income Tax and VAT returns for one user. Its apps score 4.8 on both stores. It's worth a look if you're VAT registered and want to avoid a monthly bill.

Watch out for: Zoho doesn't state CIS support on its pricing information. Check with Zoho before you rely on it for CIS deductions.

FreeAgent is one of our favourite tools for sole traders, and it's free with a NatWest, RBS or Ulster Bank business account, or Mettle. It has bank feeds and a running tax estimate. FreeAgent pays us nothing.

Watch out for: CIS is "not listed" on FreeAgent's pricing page. That doesn't necessarily mean it can't help, but you should check with FreeAgent before choosing it as a CIS subcontractor.

What should CIS subcontractors look for in MTD software?

• CIS deduction records: a clear place to record what your contractor took off, not just what hit your bank.
• Invoicing: invoices that show the gross amount and the expected deduction, if the software supports it.
• Receipt capture: photographing receipts for materials and tools on the spot.
• Mileage: logging journeys between jobs.
• A good app: you're more likely to keep up to date if you can do it from the van.

Here's an illustration. Dan is a self-employed plasterer who works for two main contractors under CIS. His gross turnover in 2025 to 2026 was £38,000 before expenses. That's over £30,000, so Dan must use MTD from 6 April 2027 (GOV.UK). He keeps his monthly CIS statements and wants to log receipts from his phone, so Xero or QuickBooks would suit him. If he wanted to pay nothing, Clear Books would also work.

How to choose MTD software for CIS work

1. Confirm CIS support first. Xero, QuickBooks and Clear Books list it. Sage needs Accounting Standard. FreeAgent and Zoho don't list it, so ask them.
2. Are you VAT registered? Avoid Xero Simple and QuickBooks Sole Trader Plus, or plan to upgrade.
3. Do you work on site all day? Choose a strong app, such as QuickBooks or Xero.
4. Do you use an accountant? Ask which software they prefer for CIS clients.

For trade-specific picks, see our guides for builders and electricians, or our wider list of the best MTD software for sole traders.

Who should not use this list?

Tide's accounting tool is also not suitable for CIS users, according to Tide, so we've left it out.

How we chose these

We started with HMRC's MTD for Income Tax software list and kept products from our main shortlist that sole trader subcontractors are likely to consider. We then checked each provider's pricing information for CIS support in October 2026, and scored them on CIS, price, app ratings, VAT and bank feeds, based on our review of features, pricing and user ratings. Affiliate commission plays no part in the order. Read how we test.