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, make sure all timesheets for the period are finalised. This includes:
approving timesheets
approving or declining leave requests
checking tax information and bank details
checking timesheet validations
Once timesheets have been finalised, go to the Timesheets tab and click Preview Export.
Step 2- Create a Pay Run
Review any export errors or warnings, confirm total hours and wages, and click Create Pay Run.
Once successful, you’ll see a confirmation screen and can go to Workforce Payroll.
Step 3 - Post a Pay Run
Go to Payroll > Run Payroll to view your exported timesheets.
To post a pay run:
Review the details of the pay run, including gross pay, deductions and National Insurance contributions.
Correct any errors that show.
If you’re paying staff for the first time, make sure leave balances and deductions are set up.
Click Post Pay Run.
Check the payment date and tax month in the Confirm Payment Date window, then click Confirm and post pay.
You’ll see Posting your pay run. Please wait... while it posts. The pay run then opens with a list of next steps.
Step 4 - Complete the next steps
Once a pay run is posted, a checklist shows at the top of the pay run, under Posted on and the posting date. It lists what’s left to do to finish this pay run, with a progress count, for example 2/5 completed. When everything’s done, it shows All steps complete for this pay run.
You can come back to the checklist at any time by opening the pay run from the Pay Runs tab.
Send payslips
Click Email payslips to email payslips to each employee’s personal email, or their login email if they don’t have one. Once payslips have been sent, you can click Resend payslips to send them again.
This step doesn’t show for test pay runs.
Pay employees
What you see depends on how you pay your staff:
Modulr: click Pay by Modulr.
BACS: click Export BACS payment file. Once the file is ready, click Download BACS file and upload it to your bank. The step is ticked once the file has been downloaded.
Neither set up: click Activity Detail Report and pay your team the net pay shown in the report. Workforce can’t track this, so it doesn’t count towards the progress total.
Submit FPS
Click Submit FPS to go to the FPS tab on the RTI page and submit the Full Payment Submission to HMRC. It isn’t a one-click submission.
The step shows a clock while you wait for HMRC, and a tick once HMRC accepts the FPS. You can then click View FPS.
You can also submit from Payroll > RTI > +Submit New FPS Request, select the pay run, then click View Details > Submit FPS Request.
Submit EPS
This step only shows on the last pay run of the tax month if you pay the Apprenticeship Levy and an Employer Payment Summary (EPS) is due. It shows the levy amount due, or says that no levy is due but an EPS is still required.
If you need an EPS for another reason, submit it from Payroll > RTI > EPS.
Click Submit EPS to go to the EPS tab on the RTI page. The step is ticked once HMRC accepts the EPS.
Pay pension contributions
NEST: click Send Contributions to Nest. The step shows a clock while you wait for the payment to be approved, and a tick once it’s approved.
Other pension providers: click Pension Contribution Report, or use the dropdown to Generate PAPDIS, and send the contributions to your provider. Workforce can’t track this, so it doesn’t count towards the progress total.
This step doesn’t show if there are no pension contributions on the pay run, unless you’re connected to NEST.
Record the journal
Click Download CSV to download the journal and import it into your accounting system. If you’ve connected Xero, click Export to Xero to send it there.
What the icons mean
Green tick: done.
Spinner: in progress, for example payslips being emailed or a BACS file being generated.
Clock: waiting on someone else, such as HMRC, Modulr approval or NEST.
Red: something needs your attention, for example HMRC rejected the FPS. Check the errors and submit it again, a failed Modulr or employee payment, or contributions NEST rejected. Fix the issue and try the step again.
Numbered circle: still to do.
Actions and Reports
Actions and Reports are at the top right of the pay run.
Reports has the Payslips, Activity Detail, Timesheet Comparison, Payment Summary by Team and Leave Accruals reports.
Actions has Bulk Upload to Payslips and Revert to draft. On a posted pay run, Actions only shows when the pay run can be reverted.
Pay run notes
You can leave notes on a posted pay run, for example to record why a payment was late. Notes are only visible to people who can view the pay run. Employees can’t see them.
Open the posted pay run.
Click Notes at the top of the page.
Type your note in Add a note for this pay run and click Add note.
Admins can manage all notes. Payroll Officers can see all notes, and edit or delete their own.
Revert a pay run to a draft
If you need to change a posted pay run, you can revert it to a draft.
To revert a pay run:
Go to the Pay Runs tab.
Open the pay run.
Click Actions > Revert to draft.
Click Revert to confirm.
Reverting reverses leave accruals. You can post the pay run again when it’s ready.
⚠️ Important: You can only have one draft pay run at a time for each pay group. If another draft exists, Actions won’t show on the posted pay run.
When you post the pay run again, the next steps start again, so you’ll need to submit a new FPS, and a new EPS or NEST contributions if they’re due. All payslips are marked as not sent, so you’ll need to email payslips again.
If you’d already paid by Modulr, the payment stays recorded and you can’t pay by Modulr again from this pay run.
If you created a BACS file before reverting, you can’t download it again. Click Export BACS payment file to create a new one.
⚠️ Important: Reverting doesn’t cancel anything already sent to HMRC, NEST or Modulr. If you’d already submitted an FPS, check the corrected FPS before you submit it.
FAQs
Why is an employee missing from my pay run?
Why is an employee missing from my pay run?
Each pay run only includes employees on the same pay group and company file as the pay run. If someone’s missing, check:
Their timesheet is approved and was included when you clicked Preview Export.
Their pay group. Open their staff profile and go to Pay Conditions > Pay Configuration > Pay group for next clock in. If you can’t see this option, see Why can’t I change an employee’s pay group? below.
They’re active. Inactive employees aren’t included.
To add them to a draft pay run, see Why can’t I add an employee to my pay run? below.
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?
If Actions doesn’t show on the posted pay run, there’s usually another draft pay run for the same pay group. Post or delete that draft first, and Actions comes back. If there’s no other draft, contact Workforce support. You also can’t revert while payslips are being emailed. Wait for that to finish, then try again.
Where has Email Payslips gone from the Actions menu?
Where has Email Payslips gone from the Actions menu?
Payslips are now sent from the Send payslips step at the top of the posted pay run. Click Email payslips, or Resend payslips to send them again.
Why isn’t a step ticked when I’ve done it?
Why isn’t a step ticked when I’ve done it?
Some steps can’t be tracked by Workforce, such as paying staff from the Activity Detail report or paying a pension provider other than NEST. These never tick and don’t count towards the progress total. For BACS, the step only ticks once the file has been downloaded. For FPS and EPS, it ticks once HMRC accepts the submission, so it shows a clock until then.
Why can’t I change an employee’s pay group?
Why can’t I change an employee’s pay group?
If your company only has one active pay group, Pay group for next clock in won’t show on staff profiles. This can leave an employee stuck on an old pay group that’s no longer active, so their timesheets don’t go into your pay run.
To move them to the right pay group:
Go to Workforce > Staff.
Tick the employee.
Click Bulk actions and select Assign employees to a pay group.
Choose the pay group and confirm.
📝 Note: Their timesheets from their next clock-in will go to the new pay group. Timesheets they already have stay on the old pay group.
Preparing for the end of the tax year? See our Payroll Year-End Guide.