FreeAgent payroll for accountants

This article explains how to set up payroll in a client’s FreeAgent account and make RTI submissions to HMRC. It also explains how to make payroll corrections.

Please note that FreeAgent's payroll functionality won't be available for clients who have unincorporated landlord accounts or prepare their accounts using cash basis accounting.

If you are currently filing your client’s payroll outside of FreeAgent and moving their payroll to FreeAgent during the tax year, find out how to move payroll to FreeAgent from another software provider.

If you are currently filing your client’s payroll outside of FreeAgent and won’t be using FreeAgent’s payroll functionality, you can record your client’s payroll by creating journal entries.

How to set up payroll

1. Add each individual as a user

In order to set up payroll in FreeAgent, each employee that will be included on your client’s payroll will need to be added as a user in your client’s FreeAgent account.

Users page listing names, positions, emails, and when last logged in.

2. Enter the client’s company details

You'll need to enter the PAYE and Accounts Office reference numbers in your client’s ‘Company Details’. If your client has a limited company account, you can also enter their Corporation Tax reference number if you wish.

PAYE reference, Accounts Office reference and Corporation tax reference highlighted in company details section.

3. Choose when to start running payroll from and add the first user

Navigate to the ‘Payroll’ area of your client’s account and choose which tax year and month you want to start running payroll from in FreeAgent.

Options to select which year and month payroll should run from on payroll page.

Next, use the drop-down menu to select the first user to add to your client’s payroll and select ‘Set up payroll’. You’ll need to add each user individually.

Options to select a user to add to payroll on payroll page.

4. Create a payroll profile for each employee on your client’s payroll

You’ll need to create a payroll profile for each employee that will be included in your client’s payroll. These will contain details of each individual's monthly pay, deductions, pension contributions and starting/leaving dates.

Monthly pay section with Basic pay, allowance, other payments and pay not subject to tax or NI.

Useful resources for setting up payroll

You might find the following articles useful for setting up payroll in your client’s account:

How to submit payroll to HMRC

Once you’ve set up payroll in your client’s account, you can prepare the payslips.

'Prepare month [x] payroll' button highlighted in payroll page header.

Then, select the payment date, edit any payslips if necessary and run and report the RTI submission to HMRC.

'Run and report month [x] payroll' button highlighted at top of prepare month [x] payroll page.

If you’re running payroll for multiple clients in FreeAgent, you can file clients’ payroll in bulk from your Practice Dashboard.

Useful resources for running payroll

You might find the following articles useful for running payroll in your client’s account:

How to make payroll corrections

Once you’ve filed payroll to HMRC using FreeAgent, it’s not possible to delete or undo the payroll submission. However, if you need to make any corrections to an employee’s pay or deductions in the current tax year after filing the payroll, you can edit the relevant payslip, which will submit the correct year-to-date figures to HMRC in your next submission.

If you need to make corrections in a previous tax year or to a month 12 payslip, find out how to make a payroll correction for a previous tax year.

How to add and remove employees from payroll

You might find the following articles useful for adding and removing employees from payroll in your client’s account:

How to access client forms

You might find the following articles useful for accessing the relevant forms in your client’s account:

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