Getting CIS deductions back once you are in MTD

acrenvo.com/guides/mtd-cis-repayment, last reviewed 12 October 2026

Sam is fictional. He is a self-employed joiner paid under the Construction Industry Scheme (CIS), and last year was quieter than usual: a run of short jobs, a few weeks without work and some expensive new tools. His contractors kept taking deductions all the same, so he suspects they add up to more than the tax he owes for the year. In the past his accountant sorted out the repayment through his Self Assessment return. Now that he sends his tax return through Making Tax Digital (MTD) software, he wants to know how the money comes back to him. This guide sets out what GOV.UK says, and where it has not yet joined the two sets of guidance together.

Why a repayment can be due

GOV.UK’s guidance on paying tax and claiming back deductions starts from what the deductions are. The deductions your contractor takes under the Construction Industry Scheme (CIS) are advance payments towards your tax. You must tell HM Revenue and Customs (HMRC) about the deductions when you report your taxes.

HMRC’s guide to CIS for contractors and subcontractors explains what happens when they come to more than the bill. If the amount already paid or deducted is greater than the amount due, HMRC will repay the excess. If there is a shortfall, then the subcontractor must make a balancing payment.

Whether Sam is owed anything depends on his whole tax position for the year, which only his return settles, and HMRC is the one that works it out. HMRC will work out how much tax you owe and take off any deductions taken by contractors. If you still owe tax after this, you’ll need to pay it by 31 January following the end of the tax year. If you’re due a tax refund, HMRC will pay the money back.

Check the deductions HMRC adds before you submit

Under MTD, the deductions reach your tax return through HMRC rather than being typed in by you. GOV.UK’s guidance on submitting your tax return says that if HMRC has information about your other income sources, HMRC will add them to your tax return for you. Its list includes “Construction Industry Scheme (CIS) — subcontractor deductions”. After HMRC has added this information, you can find it in either your software (when you ask for a calculation) or your HMRC online services account. You must check this information before you submit your tax return.

This check matters to Sam, because the deductions are tax he has already paid. His monthly statements are what he checks them against, and the guide to your monthly CIS statements explains what each one shows and what to do if one is missing.

Asking for the refund once your return has gone

GOV.UK’s MTD guidance is clear that the return itself is not where a refund is claimed. If you think you are due a tax refund, you cannot claim the refund in your tax return using Making Tax Digital for Income Tax.

Its help and support page explains the route instead. If you submitted your tax return using Making Tax Digital for Income Tax software, you need to request the refund using your HMRC online services account.

If you are unsure which applies to you, HMRC’s online services account is the place to look once your return has been submitted, and an accountant or tax adviser can check the position with you. HMRC has also said it is working on additional support for Construction Industry Scheme (CIS) customers, so this part of GOV.UK’s guidance may change. When GOV.UK makes a significant change to a page it adds a short note saying what changed, and we collect those notes in what GOV.UK changed on the pages we cite.

If you stop trading during the year

GOV.UK has a separate rule for this case. If you stop trading, you may be able to get a refund of deductions you’ve already paid this tax year. Use the sole trader or partner form to make a claim. The form is linked from GOV.UK’s page on paying tax and claiming back deductions. The guide to stopping a business or letting covers what MTD still asks of you when a business closes.

Questions about CIS repayments