How to edit or delete payroll that has been marked as filed

This article explains how to mark payroll as unfiled in FreeAgent in the current tax year so that you can edit the payslips. It also explains how to delete payroll that has been marked as filed in FreeAgent.

If you haven’t filed the payroll to HMRC and you need to make corrections in the current tax year, follow the steps below.

If you need to make corrections to payroll that has been marked as filed in a previous tax year, follow these steps instead.

Please note:

  • Don’t select the ‘Make Corrections’ button as this will prevent you from deleting any pay periods and rolling back payroll to a previous month, meaning corrections would need to be made using journal entries.

  • FreeAgent's payroll functionality won't be available if you have an unincorporated landlord account or if you're preparing your accounts using cash basis accounting.

  • You need to have full (level 8 access) to your FreeAgent account to be able to edit or delete a payroll submission that has been marked as filed.

  • If you’ve filed the payroll submission to HMRC using FreeAgent, it’s not possible to delete or undo the payroll submission. To make any corrections in the current tax year to an employee’s pay or deductions after filing the payroll, edit the relevant payslip, which will submit the correct year-to-date figures to HMRC in your next submission. To make corrections in a previous tax year, find out how to make a payroll correction for a previous tax year.

1. Navigate to the relevant pay period

Navigate to the ‘My Money’ tab at the top of the screen and select ‘Payroll’ from the drop-down menu.


Select the relevant month from the ‘History’ section.

Payroll overview screen with month highlighted in history section.png

2. Mark the pay period as unfiled

Before you can delete or make any changes to a pay period which has been marked as filed, you need to mark it as unfiled.

To do this, select ‘Mark as unfiled’ in the top-right.

Mark as unfiled highlighted.png

3. Edit the payslips or delete the pay period

Once the payroll has been marked as unfiled, you can either edit the payslips or delete the pay period.

Edit the payslips

To edit a payslip, select ‘View Payslip’ to the right of the relevant employee’s name.

View unfiled payslip.png

Next, select ‘Edit Payslip’ in the top-right.

Edit payslip highlighted.png

Make the required changes, then select ‘Save Changes’ at the bottom of the screen. Find out more about how to review and edit payslips.

To complete the process, mark the pay period as filed again.

Delete the pay period

To delete the pay period, select ‘Continue Month [X] Payroll’ in the top-right.

Continue pay period highlighted.png

Next, select ‘Delete Month [X] Payroll’. This will delete that month’s payroll, including the generated payslips. Please note that you won’t see the option to delete the pay period if there is an account lock in place or if there is an employee leaving the business who has been marked as hidden.

Delete payroll highlighted.png

Select ‘OK’ in the pop-up window to complete the process.


You can then prepare the payslips again and mark the payroll as filed if you’re filing it to HMRC outside of FreeAgent, or file the payroll to HMRC using FreeAgent.

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