How to file clients’ payroll in bulk

This article explains how you can use FreeAgent to file your clients’ payroll in bulk.

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.

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 reassign your clients to a colleague. This will allow them to file payroll for these clients in your absence.

If you have client accounts listed with the status of ‘Late’, you will need to switch to each of those client accounts individually and file the late payroll submissions from within each client account. This will allow you to complete the late submission reason dropdown option on each client’s payroll. Once the late submissions have been filed, you can follow the steps below to prepare and file any remaining payroll in bulk.

1. Navigate to payroll

Log in to your Practice Dashboard and select the ‘Payroll’ tab at the top of the screen to access the bulk payroll filing dashboard.

Payroll tab.png

2. Choose which clients to include

If there are any clients who you want to exclude from that month’s payroll run, select 'No' to the left of the client’s name. This will exclude that particular client from the month’s payroll run and all other clients will be automatically included.


To include any previously excluded clients in a future month’s payroll run, you will need to select 'Yes' to the left of the client’s name. Until you do this, these clients will remain excluded from future payroll runs.


3. Prepare and file payroll

Once you’ve excluded any clients that you don’t want to include in the payroll run, you can select either ‘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, 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.

Please note that the ‘Prepare Payslips’ or ‘Prepare & File Payslips’ options will only be visible once the relevant tax month has begun (i.e. to prepare or file Month 1, the date would have to be at least 6th April).

After you select ‘Prepare & File Payslips’, 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 in the pop-up window, select ‘Run & Report Payroll’ to complete the process. 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.

How to review 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 on the ‘Payroll’ section of your Practice Dashboard.


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


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