How Do I Pay My CIS Deductions to HMRC? (UK Companies short guide)

If you’re in the construction industry and paying subcontractors, you’ll already know about the Construction Industry Scheme (CIS)  and possibly how fiddly it feels at first.

The short version: You deduct tax from your subcontractors’ payments and pay it to HMRC on their behalf.

Sounds simple, right? In theory, yes. In reality, lots of business owners feel unsure about when, where and how to actually make the payment.

Let’s break it down together.

🧾 Step 1: Run your monthly CIS return

Every month (even if you haven’t paid anyone), you need to:

• Submit a CIS return to HMRC

• Include the details of all subcontractors paid that month

• Confirm how much tax you’ve deducted

Once submitted, HMRC will tell you what you owe.

💡 You must file the return by the 19th of the following month.

💷 Step 2: Know your payment deadline

You must pay your CIS deductions to HMRC by the 22nd of each month if paying electronically.

For example:

• CIS deductions for work done in May

• Must be reported by 19 June

• Payment due by 22 June

⚠️ Late returns or payments can lead to automatic fines, even if you’re just one day out.

💳 Step 3: How to pay your CIS bill to HMRC

HMRC doesn’t have a special payment system for CIS. You’ll pay it as part of your PAYE bill.

CIS is rolled into your employer PAYE payment using your Accounts Office Reference Number.

Ways to pay:

• Bank transfer (Faster Payments, BACS, CHAPS)
  Use your Accounts Office reference

• Business banking app
  Many let you choose “Pay HMRC – PAYE”

• Debit or corporate credit card
  Pay here

• Direct Debit
  You can set this up in your online account

🤔 Common mistakes to avoid

• Using the wrong reference — always use your Accounts Office Ref, not your VAT number or UTR

• Not paying just because no work happened — if you paid zero subcontractors, still file a nil return

• Forgetting it’s bundled in with PAYE — your PAYE bill might look higher if it includes CIS deductions

🧠 What if you’re a subcontractor?

If you’re on the other side — getting CIS deducted from your income — you don’t pay HMRC directly. But you do need to reclaim the tax through your:

• Self Assessment tax return (if self-employed)

• Monthly EPS submissions (if you’re a limited company)

Need help working out which you are, or how to reclaim properly? Book a call. We’ve got you.

✨ We keep CIS clients calm, compliant and in control

We help contractors keep on top of returns, payments and deadlines — no spreadsheets, no overwhelm, no “oh no I forgot the 19th again” moments.

If you’d rather get back to the tools while we deal with the tax, we’re your people.

Book a free call to chat through your set-up and see how we can help.