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Deleting a pay run in QuickBooks Online Standard Payroll

Things to know

  • You cannot delete just one payment in a payroll. If you delete a payroll, QuickBooks Online deletes all of the employee payments in the payroll.
  • If you're trying to correct an employee payment, you can make changes in the next payroll, The FPS for the next payroll will reflect the updates.
  • If you need to delete an entire payroll, 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 payroll.

Deleting a pay run

To delete your pay run:

  1. Go to the Employees or Payroll menu.
  2. In the Payroll History section, select the most recent period.
  3. On the Payroll details page, click Action and select Delete Payroll.
  4. Type Yes in the box, then click Delete.
  5. Repeat for any additional pay runs you require.

What happens when you delete a payroll

QuickBooks journal entries

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.

SMP/SPP: Statutory Maternity Pay and Statutory Paternity Pay

If you've already submitted an EPS that reports recovery and compensation to HMRC, we'll delete the EPS filing and prompt you to submit a new one, Go to Taxes > Payroll Tax.

Auto Enrolment

  • Any employees who has 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.

EPS for no payroll in the tax month

  • 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.

If you have any questions about leavers, contact us for help.

See also

Employees and payroll

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