Most business owners/managers want to spend as little time as possible on their admin so that they have as much time as possible to spend on running their business and generating profit. One of those mundane admin tasks, that often gets missed, is paying your PAYE to HMRC.

As PAYE payments are often required monthly or quarterly, we recommend that you set up a PAYE direct debit with HMRC to avoid late payments and to help save you time as a business owner.

The variable direct debit with HMRC for PAYE will be taken on or around 22nd of the month following the tax month/quarter based on the monthly RTI payroll submissions which Integro Accounting complete on your behalf. For example, if your quarter 4 PAYE period ends on 05/04/2026 and the payment will be paid around 22/04/2026.

You are able to setup a direct debit with HMRC here: https://www.gov.uk/pay-paye-tax/direct-debit

We have put together some helpful steps for you depending on your situation

Step 1

The first thing to do is check if you have a government gateway account. If you already have an account, please proceed to step 2.

If you do not have a HMRC online account yet:

  1. Go to HMRC Online Services and click ‘Create new sign-in details’: https://www.gov.uk/log-in-register-hmrc-online-services
  2. Enter your email address. HMRC will then send you a verification code, please enter this code to continue.
  3. Enter your name and create a password.
  4. Your User ID will be displayed on the screen – please save this information for your own records as you will need this to login in future.
  5. Select ‘Organisation’ and set up security preferences.
  6. When asked for ‘Organisation details’, select ‘PAYE for Employers’ and enter your company PAYE reference and Accounts Office reference. If you do not have these, please see later in the article for places you can find these.
  7. HMRC will send a letter in the post within 10 days containing an activation code. Once you receive the letter, log in to HMRC Online Services and enter the activation code to complete the setup. Please note that this code will last for 28 days.

Step 2

If you already have an account and PAYE services added, please proceed to step 3.

If you have a government gateway account setup but the ‘PAYE for Employers’ account is not yet added, please follow the below steps:

  1. Log in to your Government Gateway account.
  2. If PAYE for Employers is not showing on your account, click ‘Services you can add’, then select ‘PAYE for Employers’.
  3. Enter your company PAYE reference and Accounts Office reference. Please see lower in this article on places which these can be found.
  4. HMRC will send a letter in the post within 10 days containing an activation code. Once you receive the letter, log in to HMRC Online Services and enter the activation code to complete the setup. Please note that this code will last for 28 days.

Step 3

Setting Up a Direct Debit for PAYE/NI:

  1. Log in to your Government Gateway account.
  2. Navigate to ‘Employers’ PAYE’.
  3. Click on ‘Set up a Direct Debit’.
  4. Follow the instructions to provide your business bank account details and confirmation that you are authorised to set up the Direct Debit. Please review and confirm details to setup the direct debit.
  5. HMRC should send a confirmation email once the setup is complete.

Extra information:

  • Payment is usually taken around the 22nd of the month.
  • HMRC will collect the amount due for each period and will only be taken automatically if a return is submitted.
  • The direct debit only needs to be setup once, unless unused for 2 years. If unused for 2 years, you will need to check with your bank that this is still setup.
  • GOV.UK advises that you must set up the Direct Debit at least 4 working days before your first payment is due.
  • Integro Accounting are not able to set up this DD on your behalf.
  • HMRC are aware of some technical issues when setting up a ‘variable’ DD, where the is only an option to set up a ‘single payment’ DD and not ‘variable’ DD. If you experience this problem, HMRC advised to call their online services helpdesk no 0300 200 3600.

Where can I find my PAYE references?

You may already have these saved somewhere as HMRC send the references out when the PAYE scheme is setup. However, if you do not have these and you use FreeAgent for your book-keeping software, you can access these as below:

  • Login to FreeAgent
  • Click on the company name on the top right hand side of the screen and click ‘Settings’
  • Click ‘Company Details’
  • Both the PAYE reference and the accounts office reference can be found on this page.

If you use another software and you need help finding your references, please contact your accountant.