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Finalise and submit pay runs in UK EmploymentOS Payroll

Available for the following plans: Essentials, Engage, Elite, Unlimited HR+Payroll
Available on Payroll: UK Payroll
Available for the following users: Admin, users with pay run access

Finalising a pay run in UK EmploymentOS Payroll locks the pay run, updates time off balances, and enables you to submit statutory information to HMRC. This ensures payroll is complete, accurate, and compliant before payslips are published to employees.

This article explains how to:

Finalise a pay run

This section covers how to finalise a pay run, select HMRC and payslip publication preferences, and confirm the pay run is locked and complete.

Steps to finalise a pay run in UK EmploymentOS Payroll
  1. Log in to Employment Hero as an Admin or a user with pay run access.
  2. Go to Payroll > Pay runs.
  3. Select the relevant UK pay run from the list to open its details.
  4. Select Finalise pay run.
  5. In the finalisation modal, complete the following fields:
    • Date paid: Choose the date employees will be paid (defaults to the pay schedule date).
    • FPS Date: Select the date to report to HMRC (defaults to Date paid).
    • HMRC submission preference:
      • Submit now: Send the FPS to HMRC immediately as part of finalisation.
      • Submit at [date/time]: Schedule FPS submission to HMRC for a future date/time.
      • Submit manually at a later date: Do not send FPS during finalisation; you must submit it separately after finalisation.
    • Payslip publication preference:
      • Make pay slips available to employees now: Publish payslips immediately after finalisation.
      • Publish pay slips at [date/time]: Schedule payslip publication for a future date/time.
      • Do not make pay slips available until the Publish pay slips button is clicked: Hold payslips until you manually publish them later.
    • If your business has accounting integration configured, select your Journal export preference:
      • Export journals to [provider] now
      • Export journals at [date/time]
      • Do not export journals until the Export to [provider] button is clicked
    • (Optional) Tick Apply these changes to all future pay runs to save your selections as the default for future pay runs.
    • If you set payslips to "Now" or "Scheduled", choose whether to Send notifications to employees (default) or Do not send notifications.
  6. Review your selections, then confirm to finalise the pay run.
  7. A progress indicator will show while the pay run is being finalised. All actions are blocked during this time.
  8. Once complete, the pay run is locked. The page refreshes to show the finalised status and timestamp. The "Finalise pay run" button is now hidden.

Submit a pay run to HMRC after finalisation

This section explains how to submit the pay run to HMRC if you chose to submit manually during finalisation, or if the pay run was finalised before this option was available.

Steps to submit a pay run to HMRC after finalisation
  1. Log in to Employment Hero as an Admin or a user with pay run access.
  2. Go to Payroll > Pay runs.
  3. Select the relevant finalised pay run.
  4. In the post-finalisation action bar, select Submit pay run to HMRC.
  5. Wait for the progress indicator to complete. If successful, you will see a confirmation message.
  6. If HMRC rejects the submission, the reason will be shown in plain English with the HMRC reference.
  7. You can retry if there is a technical failure.

Unlock a finalised pay run

This section describes how to unlock a pay run if you need to make changes after finalisation.

Steps to unlock a finalised pay run
  1. Log in to Employment Hero as an Admin or a user with pay run access.
  2. Go to Payroll > Pay runs.
  3. Select the relevant finalised pay run.
  4. In the post-finalisation action bar, select Unlock pay run.
  5. Follow the on-screen guidance to confirm unlocking. The pay run will return to editable state.

Further information

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What happens to the pay run after finalisation?
Once a pay run is finalised, all earnings, deductions, and expenses become read-only. Actions such as deleting, recalculating, adding employees, or adjusting the pay period are hidden. The pay run header displays a finalised badge and timestamp.
Can I retry if finalisation or HMRC submission fails?
If finalisation or HMRC submission fails, you will see an error message and can retry without losing your selections. The pay run remains open until finalisation is successful.
Will employees be notified when payslips are published?
If you choose to send notifications during finalisation, employees will be notified when their payslips are published. You can also choose not to send notifications if preferred.

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