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Delete a pay run in QuickBooks Online Standard Payroll

SOLVEDby QuickBooksQuickBooks Online Payroll128Updated 3 weeks ago

Learn how to delete a pay run and understand what happens after you delete a pay run in Standard Payroll.

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

  • You cannot delete just one payment in a pay run. If you delete a pay run, QuickBooks deletes all of the employee payments in the payroll.
  • If you need to correct an employee payment, you can make changes in the next pay run and the Full Payment Submission (FPS) for the next pay run will reflect the updates.
  • Print out all the payslips and reports if you need to delete an entire pay run. This way you'll have all the info you need for all the employees you've paid when you re-create 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, contact HMRC and set up employees with a new payroll IDs. Alternatively, you can migrate to Advanced payroll.

Journal entries - QuickBooks will attempt to delete the corresponding journal entries, but there may be instances where we may not be able to, for example if your books are closed. We recommend checking your journal entries to make sure the payments have been removed.

Full Payment Submission (FPS) - QuickBooks will delete the corresponding FPS, regardless of whether it was submitted to HMRC or not.

Automatic enrolment - Any employees who have been assessed in the payroll will be reverted to their previous auto enrolment status. Be sure to contact your workplace pension provider and report your contribution amounts so they have accurate information. We recommend printing out your workplace pension reports before deleting the pay run.

EPS for no employees paid in the tax month - If you didn't pay any employees for the tax period and you submit 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.

Leavers - If the pay run includes an employee leaver and you submit an FPS to HMRC, you won't be able to edit the employee's leave date. We'll also keep their P45 in their Documents. If you did not make a submission yet, you can still edit the employee's leaver date.

Learn more about processing leavers.

How to delete a pay run

  1. Go to Payroll and select Employees (Take me there).
  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:

  • Added a new employee, delete the newly added employee before trying to roll back the pay run again.
  • Added a new pension, delete the newly added pension. If you are unable to do this please contact support for further assistance. 
  • Have any employees that have recently been added or assessed for an existing pension, make a note of the employees and reach out to support for further assistance.

See also

Employees and payroll

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