How to mark payroll as filed

This article explains how to mark payroll as filed in FreeAgent without reporting it to HMRC.

Please note that FreeAgent's payroll functionality won't be available if you have an unincorporated landlord or non-UK account type, or if you're preparing your accounts using cash basis accounting.

If you or your accountant file monthly payroll outside of FreeAgent, you can follow the steps below in FreeAgent to mirror the payslips that you submitted to HMRC and mark your payroll as filed. For information on making changes to payroll which has been marked as filed, please see this article.

Alternatively, you can enter the information by creating journal entries.

If you’re running monthly payroll and reporting it to HMRC using FreeAgent, please see this article.

Before you start

You need to have full (level 8 access) to your FreeAgent account to be able to mark payroll as filed. Please ensure you’ve completed the setup steps in this article and created a payroll profile for each employee that will be included on your payroll before following the steps below.

Prepare the payslips

Before you can mark payroll as filed for a particular pay period, you need to prepare the payslips for that period.

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


The payroll dashboard highlights recent payroll activity, displays actions that you need to take and summarises useful data for the year.

Select ‘Prepare Month [X] Payroll’ in the top-right of the screen. ‘X’ will be the number of the month for which you’re marking as filed. For example, if you’re marking as filed the first month of the tax year (6th Apr - 5th May), you’ll see ‘Prepare Month 1 Payroll’.


Payslips will be prepared for employees based on the information entered into their payroll profiles.

Run the payroll

1. Choose a date for your pay period

Next, enter the date that the business has paid, or is going to pay, its employees using the calendar.

This date defaults to the 25th for the first month you run payroll in FreeAgent. If you change this date on a submission, it will default to the new date when you prepare payroll for the following month.

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If the current month ends on the 30th and you select this date, then by default the following month will also process the payroll on the 30th. If you choose the 31st the following month, FreeAgent will recognise this and start processing subsequent payrolls at the end of the month, regardless of whether the month ends on the 28th, 29th, 30th or 31st.

2. 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. You can edit each employee's monthly pay, statutory pay, deductions, and pension contributions. Please note that any changes made here will only update the details of this month’s submission and not update the individual's payroll profile. 

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Once all of the information is correct, select ‘Save Changes’.

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3. Double-check everything

Using the checklists provided, make sure that you’ve made any necessary changes to your payroll profiles such as adding employee leaving dates, making changes to tax codes or updating student loan settings. Also, make sure that all of your employees are included on the payroll and that the payslips are correct for each employee who is receiving a salary payment this month.

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4. Mark the payroll as filed

Finally, scroll down and select the check box next to 'Don't report Month [X] payroll to HMRC' at the bottom of the screen. Then, select ‘Run Month [X] Payroll’ to complete the process.

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What happens next?

FreeAgent will mark your payroll as filed and you will see confirmation of this in the ‘Payroll Summary’ panel in FreeAgent.


If you need to make any changes after marking payroll as filed, please see this article.

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