How to prepare and run payroll

This article explains how to report monthly PAYE information to HMRC in real time using FreeAgent’s payroll functionality.

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.

If you or your accountant file payroll outside of FreeAgent, you can mark your payroll as filed instead of following the steps below.

Before you start

If you have employees or you’re paid a salary as a limited company director, you must register as an employer with HMRC before making your first RTI submission.

You need to have full (level 8 access) to your FreeAgent account to be able to prepare and run payroll. 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.

Please note that there are two different types of RTI submissions which should be filed at different times:

  • If you're paying employees, an FPS and EPS submission can be submitted from the beginning of the month. For example, if you’re filing Month 1 payroll, this can be submitted from 1st April.

  • If you're not paying employees and try to submit an EPS before the beginning of the tax month, e.g before 6th April if you’re filing Month 1 payroll, you’ll receive an error message. You’ll then need to go back into the payroll month after the beginning of the tax month and run the payroll again to file the EPS submission.

How to prepare payroll

Prepare the payslips

Before you can file payroll for a particular pay period to HMRC, you need to prepare your employees’ 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 filing payroll. For example, if you’re filing payroll for 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.

How to run payroll

To run payroll, you'll need to choose a date for your pay period, review the payslips and double-check everything is correct.

1. Choose a date for your pay period

Next, enter the date that the business is going to pay its employees using the calendar. HMRC requires that the RTI submission is made on or before this date. Ensure that this date is correct before filing the payroll.

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’.


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. 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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Please note that if you or your accountant file payroll outside of FreeAgent, you can mark payroll as filed in FreeAgent without making an RTI submission to HMRC by ticking the ‘Don’t report Month [X] payroll to HMRC’ box.

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

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Next, enter your 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 and you will see confirmation of this in the ‘Payroll Summary’ panel in FreeAgent. Find out how to download a copy of the data submitted to HMRC.

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Find out how to explain a salary payment to an employee.

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