How to file missing payroll submissions after the end of a tax year

This article explains how to file missing payroll submissions for the previous tax year after the year-end deadline date of 19th April.

Please note that 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.

For tax years up to and including 2019/20, employers could use an Earlier Year Update (EYU) to make amendments to their payroll submissions. However, from the 2020/21 tax year (the tax year ending 5th April 2021), any amendments or late submissions will need to be made using a further 'Year to date (YTD) Full Payment Submission (FPS)'.

Please note that this article details how to file an FPS for a missing pay period. In order to file a missing payroll submission after the deadline date of 19th April, you will need to have filed at least one month’s payroll for an earlier period in the previous tax year through your FreeAgent account.

If you need to make corrections after all payroll submissions have been made for the previous tax year, find out how to make a payroll correction for a previous tax year.

Before you start

Make sure that you've added all the employees who will be included on the payroll submission to your FreeAgent account as users and that you’ve created payroll profiles for them.

You need to have full (level 8) access to file payroll using FreeAgent.

1. Navigate to 'Payroll'

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


2. Prepare the payslips

Before you can file payroll for a particular pay period to HMRC, you need to prepare the payslips for that period.

To do this, select ‘Prepare Month [X] Payroll’ in the top-right of the screen. ‘X’ will be the number of the earliest month for which you haven’t yet filed payroll. For example, if you haven’t filed payroll for months 11 and 12, you’ll see ‘Prepare Month 11 Payroll’ first. After you’ve filed month 11, you can repeat the process below to file payroll for month 12.


3. Review the payslips

Check that the information on the payslips is correct.

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

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Once the figures are correct, select ‘Save Changes’ to complete the process.


4. Select a reason for the late submission

For each employee, select a reason for the late submission using the drop-down menu beside their name.

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5. File the payroll to HMRC

Once you have entered all the required information, select ‘Run & Report Month [X] Payroll’ at the bottom of the screen.

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Alternatively, select ‘Run & Report Month [X] Payroll' in the top-right of the screen.

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Next, enter your business's Government Gateway credentials in the pop-up window and select ‘Run & Report Payroll’ to complete the process.

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What happens next?

FreeAgent will submit your payroll to HMRC for the previous tax year as a Full Payment Submission. You will see confirmation of this in the ‘Payroll Summary’ panel in FreeAgent.

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