Paying CIS Deductions to HMRC

Key facts

CIS deductions must be paid to HMRC monthly, by the 19th (post/cheque) or 22nd (electronic) of the following month.
Payments use the same Accounts Office Reference as your PAYE.
CIS deductions can be offset against the contractor’s own PAYE/NIC liabilities if the contractor is also an employer.
Payment methods include direct debit, online banking, BACS, CHAPS, and cheque.
Late payment attracts interest and may trigger penalties.

Payment Deadlines

CIS operates on monthly tax months that run from the 6th of one month to the 5th of the next. Deductions for each tax month must be paid to HMRC by specific deadlines:^[2]

Payment Method	Deadline
Cheque (post)	19th of the month following the tax month
Electronic payment (online banking, BACS, direct debit)	22nd of the month following the tax month
CHAPS (same-day)	22nd of the month following the tax month

Example Tax Month Timeline

Tax Month	Period	Postal Deadline	Electronic Deadline
Month 1	6 Apr – 5 May	19 May	22 May
Month 2	6 May – 5 Jun	19 Jun	22 Jun
Month 3	6 Jun – 5 Jul	19 Jul	22 Jul
Month 12	6 Mar – 5 Apr	19 Apr	22 Apr

Tip: If the deadline falls on a weekend or bank holiday, the payment must reach HMRC on the last working day before the deadline. Set up reminders or, better still, use a direct debit to ensure payments are never late.

How to Pay

HMRC accepts CIS payments through several channels:^[1]

Method	Processing Time	Notes
Direct debit	Automatic on due date	Set up through HMRC online services; most reliable option
Online banking / Faster Payments	Same day or next day	Use HMRC’s bank details and your payment reference
BACS	3 working days	Allow time for processing before the deadline
CHAPS	Same day	Usually a fee charged by your bank; good for last-minute payments
Cheque by post	Allow 3+ working days	Must reach HMRC by the 19th; post early

Your Payment Reference

CIS deductions are paid using the same Accounts Office Reference as your PAYE. The reference is a 13-character code (e.g. 123PA00012345) followed by a 4-digit period indicator.^[1]

You can find your Accounts Office Reference:

In your HMRC online business tax account
On the P30BC (Employer Payment Booklet) that HMRC sends at the start of each tax year
On any HMRC correspondence about your PAYE scheme

Important: Using the wrong reference can result in your payment not being allocated to your account. Always double-check the reference, especially the period indicator, before making each payment.

CIS and PAYE: Combined Payments

If you are both a CIS contractor and a PAYE employer, your CIS deductions are combined with your PAYE/NIC liabilities into a single monthly payment to HMRC:^[2]

Liability	Amount
PAYE tax deducted from employees	£3,000
Employer NICs	£2,500
Employee NICs	£1,800
CIS deductions from subcontractors	£1,200
Total payable to HMRC	£8,500

You make one payment of £8,500 using your Accounts Office Reference. HMRC allocates the amounts internally based on your RTI submissions and CIS returns.

Offsetting CIS Deductions Suffered

If you are a contractor who also works as a subcontractor (and has CIS deductions taken from your own payments), you may be able to offset the CIS deductions you have suffered against the CIS deductions and PAYE/NICs you owe to HMRC. This can reduce your monthly payment.^[2]

For limited companies, CIS deductions suffered can be offset against PAYE, NICs, student loan deductions, and CIS deductions due. Any excess can be repaid or carried forward.

Quarterly Payment Option

Small employers may qualify to pay PAYE and CIS deductions quarterly instead of monthly. You may be eligible if your average total monthly payments to HMRC (PAYE + CIS combined) are less than £1,500. HMRC will notify you if you qualify for quarterly payments.^[3]

Quarterly payment deadlines are:

Quarter 1 (Apr–Jun): 19 July (post) / 22 July (electronic)
Quarter 2 (Jul–Sep): 19 October / 22 October
Quarter 3 (Oct–Dec): 19 January / 22 January
Quarter 4 (Jan–Mar): 19 April / 22 April

Consequences of Late Payment

Paying CIS deductions late has financial consequences:

Interest: HMRC charges interest on late payments from the date they were due until the date they are received
Penalties: Persistent late payment can trigger in-year penalties under the PAYE penalty regime
Compliance risk: Repeated late payments may prompt HMRC to open a compliance check into your CIS affairs

Frequently Asked Questions

When do I need to pay CIS deductions to HMRC?

CIS deductions for a tax month (6th to 5th) must be paid to HMRC by the 19th of the following month if paying by cheque or post, or by the 22nd if paying electronically. For example, deductions for the tax month 6 April to 5 May must be paid by 19 May (post) or 22 May (electronic).

Can I offset CIS deductions against my PAYE bill?

Yes. If you are also a PAYE employer, CIS deductions are paid together with your PAYE and NICs liability. The total amount you owe HMRC each month is your PAYE/NIC plus CIS deductions, and you can make a single payment covering both.

What payment reference do I use?

Use your 13-character Accounts Office Reference followed by the relevant tax period. This is the same reference you use for PAYE payments. You can find it on letters from HMRC or in your online business tax account.

What happens if I pay late?

Late payment of CIS deductions attracts interest from the date the payment was due. Repeated late payments may also result in penalties. HMRC may also take enforcement action if significant amounts remain unpaid.

Sources

Pay CIS deductions to HMRC — GOV.UK
What you must do as a CIS contractor — GOV.UK
CIS: payment deadlines — GOV.UK