What’s covered in this guide?
Run Payroll
Before you run payroll, you will need to configure your account. See our Payroll Setup Checklist guide to learn more.
Step 1 - Review Timesheets
At the end of each pay cycle, ensure all timesheets for the period are finalised. This includes:
Approving timesheets
Approving or declining leave requests
Validating tax information and bank details
Validating checks for timesheets
Once timesheets have been finalised, navigate to the Timesheets tab and click the Preview Export button.
Step 2- Create a Payrun
Review any export errors or warnings, confirm total hours and wages, and click the Create Pay Run button.
Once successful, you’ll see a confirmation screen, and can navigate to Workforce Payroll.
Step 3 - Post a Pay Run
Navigate to Payroll > Run Payroll to view your exported timesheets.
To post a pay run:
Review details of the pay run including gross pay, deductions, National Insurance contributions, and other details.
Correct any errors that may display
If paying staff for the first time, ensure leave balances and deductions are configured
Once satisfied with the pay run, click Post Pay Run
Step 4 - Submit to HMRC
After posting the pay run, you can submit the FPS in two ways:
From the posted pay run’s page, click the Submit FPS request link. This takes you to the RTI page to complete the submission, it isn’t a direct one-click submission.
2. Alternatively, navigate to Payroll > RTI > +Submit New FPS Request > select a pay run from the dropdown menu > View Details > Submit FPS Request.
Address any errors returned in real time and resubmit as necessary.
Email payslips
After posting the pay run, you can email payslips to employees in two ways:
From the pay run confirmation screen, select the dropdown next to Back to Pay Run. Choose Email Payslips to send electronic copies to the email addresses listed in each employee’s Workforce profile.
2. Alternatively, you can email payslips by navigating to Pay Runs > Select the pay run > Actions > Email Payslips.
Revert a pay run to a draft
If changes are required to a posted pay run, you can revert it to a draft as long as the Full Payment Submission (FPS) has not yet been submitted to HMRC.
To revert a pay run:
Navigate to the Pay Runs tab
Open the relevant pay run
Click Actions > Revert to draft
Confirm the action by selecting REVERT on the confirmation message
⚠️ Important: you can only have one draft pay run at a time for a given pay schedule, reverting will fail if another draft already exists for that period.
FAQs
Why is an employee missing from my pay run?
Why is an employee missing from my pay run?
Check these, in order:
They’re on a different pay group. A pay run only includes employees on that pay run’s pay group, for example Weekly or Monthly. Open their staff profile, go to Pay Conditions > Pay Configuration and check Pay group for next clock in.
Their timesheet wasn’t approved or exported. Hours only reach payroll from approved timesheets. Approve the timesheet. If there’s no draft pay run for this pay group yet, go to Timesheets > Preview Export and click Create Pay Run. If the draft pay run is already open, open the employee’s timesheet and use Export to... to add it to that draft.
They’re salaried but have no salary template. Salary is only added automatically if the employee has a salary template under Autopaid Salary Earnings on their staff profile’s Payroll tab, and only on In Cycle pay runs.
Their employment dates don’t cover the pay period, or their profile is inactive.
They’ve already been paid in another pay run for the same period.
They’re on a different company file. If your organisation has more than one company file, each pay run only includes employees on its company file.
Why can’t I add an employee to my pay run?
Why can’t I add an employee to my pay run?
On a draft pay run, + Add employee only lists active employees who are on the same pay group and company file as the pay run, and who aren’t on it already. You also need permission to edit that employee. If they’re not in the list, check their Pay group for next clock in and their company file.
Adding someone this way gives them an empty payslip, or their salary if they’re salaried on an In Cycle pay run. Their timesheet hours aren’t brought across. For hourly staff, approve their timesheet and use Export to... on the timesheet instead
Why is the Create Pay Run button greyed out?
Why is the Create Pay Run button greyed out?
If you hover over it and see Draft pay run exists, there’s already a draft pay run for that pay group and company file. It may be for an earlier pay period. The Preview Export page names it and has a View Pay Run link. Post or delete that draft, then export again.
Why do only a few employees show when I run weekly payroll?
Why do only a few employees show when I run weekly payroll?
Each pay run is for one pay group. Only employees on the Weekly pay group appear in a weekly pay run. Employees on Fortnightly, Monthly or other pay groups appear in those pay runs instead. Check an employee’s pay group in their staff profile under Pay Conditions > Pay Configuration > Pay group for next clock in.
My employee’s timesheets are weekly but they should be fortnightly or monthly. How do I change it?
My employee’s timesheets are weekly but they should be fortnightly or monthly. How do I change it?
The timesheet period comes from the employee’s pay group:
Open their staff profile and go to Pay Conditions > Pay Configuration
Change Pay group for next clock in to the right pay group
Click Update Employee Details
Timesheets that already exist stay on the old pay group. New timesheets use the new pay group from their next clock-in on or after its start date. Pay runs use the new pay group straight away, so a salaried employee won’t be paid automatically in the old pay group’s next pay run.
If you can’t see Pay group for next clock in, your organisation only has one pay group. You also need permission to edit the employee’s wages. You can’t change a pay group’s frequency once it’s in use. To use a different frequency, an Admin or Payroll Officer creates a new pay group in Settings > Timesheets > Manage pay periods, then moves employees onto it.
It won’t let me post the pay run because of errors for some employees. What do I do?
It won’t let me post the pay run because of errors for some employees. What do I do?
If you see Address all errors to post your pay run, the pay run lists Payroll details are missing for those employees. Click each employee to see what’s missing, then fix it on their profile. Common errors are:
no tax code, or an invalid one
no National Insurance category
no bank account
no tax declaration
If you need to pay everyone else now, open that employee’s payslip on the draft pay run, click Actions > Delete payslip, then post the rest. Once their details are fixed, pay them in another pay run. In an out-of-cycle pay run their salary and timesheet hours aren’t added automatically, so you’ll need to add their pay to the payslip yourself.
Why can’t I revert my pay run to draft?
Why can’t I revert my pay run to draft?
Revert to draft isn’t shown in the Actions menu while there’s another draft pay run for the same pay group. Post or delete that draft first, and the option comes back. You also can’t revert while payslips are being emailed. Wait for that to finish, then try again.
Preparing for the end of the tax year? See our Payroll Year-End Guide.