1. Go to Summary or Pay Runs, then select Process Pay Run for the relevant pay cycle.
2. Check the pay date is correct. Edit, if required.

 TIP: If required, you can change the current pay run. See our article skip or miss a pay run.

3. Select Next.

4. To record an absence, select the relevant employee then select Add Absence.
5. Select the relevant absence type, then record the employee absence. Select Save. Repeat for any other employees then select Next.
6. Select an employee whose pay details you want to review or edit.

The information you entered for the last pay run appears. If the payment and deduction values are accurate, move to step 10.

7. To edit or enter payment details, do one of the following:

Enter a payment value	Depending on the type of payments you have, enter 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, select Add Payment. Next, select 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, select Add Payment. Then select Add a new payment and enter the relevant details.
Remove a payment	To remove a payment you don’t want to use for the current pay run, select the discard button next to the relevant payment.  TIP: This doesn’t delete the payment type. It only removes the payment type from this employee.

8. 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, select Add Deduction. Next, select the required deduction and enter the deduction amount.
Add a new deduction	If you need to use a deduction that’s not already set up, select Add Deduction. Then select Add a new deduction and enter the relevant details. For Stakeholder Pension deduction types, select a fixed amount or percentage of pay. This determines the deduction amount.
Remove a deduction	Remove a deduction from an employee’s pay in the current pay run if needed. Select the discard button next to the deduction.  TIP: Note: This doesn’t delete the deduction type. It only removes the deduction type from this employee.

9. If the employee is not due any money in the current pay run select the Exclude Employee check box. If you don't choose the Exclude Employee option the system might calculate a tax rebate. This is because it assumes the employee worked but earned nothing.

    TIP:  Please be aware that the Exclude Employee option might not be available. A correction in the employee payment page is the cause. Read our article Understanding payroll corrections (opens in new tab).

10. Repeat for each employee whose pay details you want to review or edit and then select Next. The Confirm pay window appears.

11. Once you’ve confirmed the pay values are correct, select Complete Pay Run.

The Confirm Pay Values option appears. If required, you are prompted for your company details and Government Gateway credentials (opens in a new window).

 TIP: If you’ve entered your details before and chose to store the information, then these don’t appear. To re-enter these details, select the green  Change option. 

12. Enter or check your details, then select Submit.

The FPS submits and a summary of the completed pay run appears. The FPS submission confirmation shows on the Summary tab page.

 CAUTION: If the submission fails, check the error code and resolve the issue. Read the article Submission errors (opens in new tab).

 TIP: If you have linked Payroll and Accounting, your staff payments post to your accounts. This requires you to have an Accounting subscription. 

13. Choose to print or email your payslips.

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