How do I pay HMRC?

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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.


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.



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 the OK button. 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. A message appears stating: Creating a new Payment Run will overwrite Payment Run number ... Do you wish to continue? Click Yes if you have not already sent your file. But 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?
  7. Click the Authorise Run button and confirm. Note: 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 message appears stating: HMRC BACS processing file has been generated successfully.
  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?
    • Send the payment to HMRC manually via your online banking system, by picking up the file from the BACS File location.

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