Process a pay run

You have everything you need to process a payroll. From calculating pay to printing payslips and submitting your forms to HMRC, you can do it all in just a few steps.

Process a pay run

  1. Go to Summary or Pay Runs, then click Process Pay Run for the relevant pay cycle.
  2. Check the pay date is correct. Edit, if required.
If required, you can change the current pay run which skips pay runs.
  1. Click Next.
  1. To record an absence, select the relevant employee then click Add Absence.
  2. Click the relevant absence type, then complete the relevant details and click Save. Repeat for any other employees then click Next.
  3. Select an employee whose pay details you want to review or edit.

The information you entered for the last pay run automatically appears. If the payment and deduction values are the same for this pay run and the information is correct, proceed to step 12.

If you need to, you can change certain employee tax details within this window.
  1. To edit or enter payment details, do one of the following:
Enter a payment value Depending on the type of payments you have, enter either the hours and rate. Or, if it’s a salary payment, just the rate.
Add an existing payment If you’ve set up a new payment and need to add this to the employee’s pay this pay run, click Add Payment, then click the required payment and enter the relevant amounts.
Add a new payment If you need to use a payment that’s not already set up, click Add Payment, then click Add a new payment and enter the relevant amounts.
Remove a payment

To remove a payment you don’t want to use for the current pay run, click the discard button next to the relevant payment.

This doesn’t delete the payment type.
  1. To edit or enter deduction details, do one of the following:
Enter a deduction value If applicable, enter the amount of the deduction.
Add an existing deduction To add an existing deduction to the employee’s pay in this pay run, click Add Deduction, then click the required deduction and enter the relevant amount.
Add a new deduction If you need to use a deduction that’s not already set up, click Add Deduction, then click Add a new deduction and enter the relevant amount.

For Stakeholder Pension deduction types, select fixed amount or percentage of pay. This determines the deduction amount.
Remove a deduction

To remove a deduction from an employee’s pay in the current pay run, click the discard button to the left of the deduction.

Note: This doesn’t delete the deduction type.
  1. If the employee is not due any money in the current pay run click the Do Not Pay check box. Failing to select the Do Not Pay option when the employee’s salary is zero may result in the system calculating a tax rebate as the software will assume that the employee has worked but earned zero.
    Please be aware that the Do Not Pay option won’t be available if there is a correction when processing the pay run.
  1. Repeat for each employee whose pay details you want to review or edit and then click Next. The confirm pay window appears.
  1. Once you’ve confirmed the pay values are correct, click Complete Pay Run.

The Confirm Pay Values? option appears and prompts you for your company details and Government Gateway credentials.

If you’ve entered your details before and chose to store the information for future submissions these don’t appear. To check the details are correct clear the Use saved HMRC login check box.
  1. Enter or check your details, then click Confirm.

The FPS submits automatically and a summary of the completed pay run appears. If the submission fails you should check the error code and resolve it.

If you also subscribe to both Payroll and Accounting, and have enabled payroll integration your staff payments posts to your accounts.
  1. Choose to print or email email your payslips: