Payroll - Frequently Asked Questions

This article answers the most common questions about payroll.

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.

Do I have to run payroll?

You don't need to set up payroll if you don’t have any employees and the company doesn’t pay you a salary. If the company has a PAYE scheme (e.g. because the company is reimbursing expenses) then you should be running payroll and filing RTI.

Find out how to prepare and run payroll in FreeAgent.

Can I use other payroll software with FreeAgent?

You might have previously used FreeAgent's payroll alongside another payroll system. You can continue to do this and create payslips in FreeAgent but not file them. Alternatively, you can record payroll by creating journal entries.

Can I only run payroll one month at a time?

FreeAgent currently only supports monthly payroll. It’s likely that you’ll need to make adjustments to your payroll throughout the year eg. employees leaving/new employees starting work or changes to items like overtime, commission or bonuses.

Why can't I see the button to file my payroll?

The button will appear on each pay period from the 1st of each month.

Do I need to tell HMRC it’s the final submission for the tax year?

HMRC requires you to put ‘Yes’ in the ‘Final submission for year’ field (if available) in your payroll software. FreeAgent does this automatically for you when you file month 12.

How do I close my payroll scheme?

You can submit an Employer Payment Summary (EPS) in order to close your payroll scheme. Find out how to close your payroll scheme using FreeAgent.

New or existing employee?

When first setting up your payroll in FreeAgent at the start of the tax year (eg. starting 6th April 2021) add any existing members of staff as ‘existing employees’ when creating their payroll profiles.

If an employee joins the company sometime during the tax year, add them as a ‘new employee’. Find out how to add a new employee to payroll in FreeAgent.

How do I mark an employee as having left the company?

If an employee leaves the company and you need to remove them from the payroll, you simply need to edit their payroll profile and add a leaving date. Once this leaving date is sent to HMRC this user cannot be paid again, so please don't enter the leaving date in the profile until either you have paid your employee for the last time or you intend to do so in the current pay period. Remember to pro rata the final payslip if required.

FreeAgent will include the leaving details in your next RTI submission to HMRC. Find out how to remove an employee from your payroll when they leave your business.

If a former employee returns to my business, how do I add them back to the payroll?

If the employee returns in the same tax year as they left your business, you should add them as as a new user, then create a new payroll profile for them. You shouldn't use their existing payroll profile. If the employee returns in a future tax year, however, you should use their existing user and payroll profiles.

Find out how to add a returning employee to payroll in FreeAgent.

What is RTI?

RTI stands for Real Time Information and it's the way to report wages, salaries, PAYE and National Insurance to HMRC. It requires data to be submitted to HMRC online whenever employees are paid.

Find out the difference between RTI, FPS and EPS payroll submissions.

How does RTI work in FreeAgent?

FreeAgent will submit your RTI for you as part of your payroll. You'll need to enter your Government Gateway ID details when prompted after running each monthly payroll.

Find out how FreeAgent supports RTI.

What gets sent to HMRC in my RTI submission?

For an RTI submission to HMRC, FreeAgent will send information you've entered into each individual payroll profile, payslip information (including Tax and NI calculations) and also some of your company information.

Can my accountant run payroll and submit RTI?

If your accountant is a user of your FreeAgent account (with the user type 'Accountant') they can run your monthly payroll and make RTI submissions using their HMRC agent login details.

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