---
title: "How do I pay HMRC?"
slug: "how-do-i-pay-hmrc"
updated: 2026-06-10T11:24:59Z
published: 2026-06-10T11:24:59Z
canonical: "help.cintra.co.uk/how-do-i-pay-hmrc"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://help.cintra.co.uk/llms.txt
> Use this file to discover all available pages before exploring further.

# How do I pay HMRC?

Within **Cintra iQ,** you can create payment runs to pay tax, employee and employer NI, and student loan deductions to **HMRC**. The payment runs are created by the **P32** period. Therefore, if you have more than one payroll under a tax reference, all payments due to **HMRC** are created in one run. As part of this process, the **EPS (Employer Payment Summary)** file is created and submitted to **HMRC**. The **EPS** file displays employer payments that are due such as tax, **NI** etc.

> [!NOTE]
> **Note:** You cannot perform multiple payment runs for one EPS. If any changes are required, you can include the change after the 6th of the month in the new tax period.

> [!NOTE]
> **Note:** As per HMRC regulations, you must submit an EPS every month, even if no payments are made. For example, if you pay annually, you must submit a null EPS for the months where no payment is due, then an actual EPIS in the month employees are paid.

## To pay HMRC

1. Navigate to the **Pay HMRC** window.
  - Go to **Cintra iQ**: Payroll > Payroll Tools > Paying Out > Pay HMRC
2. Select the desired **P32 Period**.
3. Click the **Create Runs** button. The information pop up appears stating: **Payment Run Created**.
  - If the entire amount of the Apprenticeship Levy Allowance has not been allocated, a message appears and prevents the Run from being created.
4. Click **OK**. The payment run for each **Employer** in the system is generated.
5. Select the desired file that you wish to send to **HMRC**.
  - To help with selecting a file, use the scroll bar at the bottom to show more information including the account name.
  - To recreate the payment run, click the **Create Runs** button again, then **Yes** if you have not already sent your file. However, if you have authorised and already sent your file, it will not be recreated.
6. Click the **Adjustments** button if necessary. The **Adjustments** window displays the details of the payment run, and allows you to claim the **Employment Allowance** and make any other adjustments.
  - For more information about **Other Adjustments**, see [How do I make other adjustments?](/iq/docs/how-do-i-make-other-adjustments-to-hmrc-payments)
7. Click the **Authorise Run** button, then **Yes** to confirm.
  - Before you close off the **Run**, it is best practise to cross check the value of the **P32** report and the value of the **Payroll Analysis** report minus the **Apprenticeship Levy** to see if there is any discrepancy.
8. Click the **Close Off** button and confirm.
9. Click the **Submit EPS** button. The **EPS** is submitted to **HMRC**.
10. Click the **Create BACS** button.
11. Amend payment details if necessary, for instance if the pay date is a weekend.
12. Click the **Create File** button. A successful message will appear.
13. Click the **OK** button. The **HMRC BACS** processing file is created and stored in the **BACS File** location displayed in the **Process BACS for HMRC Payments** form.
  - The location of BACS File depends on how your system is set up. For more information, contact Cintra's Support team.
14. Once the **HMRC BACS** processing file is created, perform either of the following:
  - View the file’s **Audit Report** by clicking on the **View Audit** button.
  - Send the file to **Cintra** for processing on your behalf, by clicking the **Transmit** button. For more information, see [How do I transmit BACS files using Cintra secure online server?](/iq/docs/how-do-i-transmit-bacs-files)
  - Send the payment to **HMRC** manually via your online banking system, by picking up the file from the **BACS File** location.

## Resubmitting an FPS

You no longer need to raise a support ticket to re-submit the last EPS. If you completed your EPS submission to HMRC and need to send updated figures you can right-click on the HMRC payment run and select ‘Re-submit EPS.

> [!NOTE]
> **Note:** This feature is only available on the most recent EPS submission and not for previous periods.

![](https://cdn.document360.io/fc2cda72-4645-4b36-96bf-60439ec11f11/Images/Documentation/ObchDF3qRqn_6Ny4Qi4B3NyItjiO9uKo3w.png)