Showing results for 
Search instead for 
Did you mean: 
Get your Payroll questions answered by a QuickBooks Product Manager here -

Delete a pay run in QuickBooks Online Standard Payroll

In this article you'll learn how to delete a pay run, and understand what happens when a pay run is deleted in QuickBooks Online Standard Payroll.

The Pay History dashboard will show the most recent pay runs by default. To access and see all pay runs in QuickBooks, go to Payroll > Pay History.


  • You cannot delete just one payment in a pay run. If you delete a pay run, QuickBooks Online deletes all of the employee payments in the payroll.
  • If you're trying to correct an employee's payment, you can make changes in the next pay run, the Full Payment Submission (FPS) for the next pay run will reflect the updates.
  • If you need to delete an entire pay run, be sure to print out all the payslips and reports beforehand. Then you have all the information you need for all the employees you've paid when you recreate the pay run.
  • If you need to delete a scheduled pay run that has already been submitted to HMRC, you can create a new pay schedule and add employees with the same payroll ID. If this doesn't work, you may need to contact HMRC and set up employees with a new payroll IDs on the new pay schedule. Alternatively, you can migrate to Advanced payroll.

We attempt to delete the corresponding journal entries in QuickBooks, but we may not be able to if, for example, your books are closed. You'll need to

check your journal entries

to make sure the payments have been removed.

We'll delete the

FPS from QuickBooks

, whether or not it was submitted to HMRC.

  • Any employees who have been assessed in the payroll will be reverted to their previous auto enrolment status.
  • If you've reported contribution amounts to your workplace pension provider, be sure to contact your provider so they have accurate information. We recommend printing out your workplace pension reports before deleting your payroll.
  • If you didn't pay any employees for the tax period and submitted an EPS to notify HMRC, we'll delete the EPS filing and prompt you to create a corrected filing.
  • If you create a new payroll with employee payments for the period, the FPS will override the EPS on record with HMRC.

If the payroll includes a leaver and you:

  • Submitted a filing to HMRC, you won't be able to edit the leaver date for the employee. We'll also keep the employee's P45 in their Documents.
  • Have not submitted an FPS yet, you can still edit the employee's leaver date.

Learn more about processing leavers here.

How to delete a pay run

To delete a pay run:

  1. Go to Employees or Payroll menu.
  2. Select Payroll History and choose the most recent period.
  3. On the Payroll details page, click Actions and select Delete Payroll.
  4. Type YES in the box, then click Delete.
  5. Repeat these steps for any additional pay runs that need deleting.

If you see the error message "Something went wrong. Please wait a moment and try again. If the problem continues, contact us." when trying to roll back a previous pay run, it may be due to the recent changes that you have made to your payroll.

Here are some reasons why it may be happening and how you can fix it:

  • If you've added a new employee

Delete the newly added employee before trying to roll back the pay run again.

  • If you've added a new pension

Delete the newly added pension. If you are unable to do this, please contact support for further assistance. 

  • If you have any employees that have recently been added or assessed for an existing pension

Make a note of the employees and please reach out to support for further assistance.

See also

Employees and payroll

Was this helpful?

You must sign in to vote, reply, or post

Need to get in touch?

Contact us