Knowledge Base Getting Started Frequently Asked Questions

Bulk payroll filing

In this article we explain how to use FreeAgent’s bulk payroll filing functionality for accountants.

Bulk payroll filing allows account managers to prepare and file RTI payroll on behalf of multiple clients in a single payroll run. Bulk payroll filing is available for all companies that are set as ‘active’ clients in FreeAgent and have at least one active payroll profile.

NB: Please note that you can only use this functionality on behalf of the clients assigned to you in FreeAgent. If you plan to be away from the office during a payroll run, we recommend that you temporarily re-assign your clients to a colleague in your absence. This will allow them to file payroll for these clients in your absence.

Getting started

To use the bulk payroll filing functionality, start by selecting ‘Payroll’ on your Practice Dashboard to access the bulk payroll filing dashboard.


Choosing which clients to include

If there are any clients who you want to exclude from that month’s payroll run, simply click on the tick icon to turn it into a cross. This will exclude that particular client from the month’s payroll run; all other clients will be automatically included.

If you want to include any previously excluded clients in a future month’s payroll run, you will need to click on the cross icons next to the relevant entries on the payroll dashboard and switch them back to ticks. Until you do this, these clients will remain excluded from future payroll runs.


Preparing and filing payroll

Once you’ve excluded any clients that you don’t want to include in the payroll run, you have two options: you can either select ‘Prepare Payslips’ or ‘Prepare & File Payslips’.


Selecting ‘Prepare Payslips’ generates payslips for your clients and allows you to review all the details for that month’s payroll before you file, including your clients’ tax figures. You might want to give your clients the chance to double-check this information before filing. When you and your clients are happy with the information you’ve reviewed, select ‘Prepare & File Payslips’ to file on behalf of all the clients you’ve included in that month’s payroll run.

Alternatively, if you are confident that payroll for that month has been set up correctly and you don’t need to review your clients’ tax figures, you can prepare and file payroll on behalf of all your selected clients in a single step by selecting ‘Prepare & File Payslips’ immediately.

NB: Please note that you will only be able to complete the ‘Prepare Payslips’ or ‘Prepare & File Payslips’ step once the relevant tax month has begun (ie. to prepare or file Month 4 the date would have to be at least the 6th of July).

Whether you select ‘Prepare & File Payslips’ at the start of the process or after you’ve reviewed your client’s payroll information, you will be prompted to select a payment date for the payroll run and to enter your Government Gateway login credentials. Please note that you can only submit payroll in bulk through FreeAgent if you have been set up as an agent with HMRC.


Once you’ve entered these details and selected ‘Run & Report Payroll’, FreeAgent will file payroll on behalf of all the clients you’ve included in that month’s payroll run and will submit their RTI data to HMRC.

Reviewing the progress of your submissions

After you’ve selected ‘Prepare & File Payslips’, FreeAgent will send each client’s payroll submission as part of a batch and will indicate how many submissions have been accepted or rejected. These figures will update in real time.


You can also check on the status of each payroll submission by using the ‘Show’ drop-down menu and selecting the relevant filter option:


Did you find this article useful?

I need help with…

View all categories →