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Delete a pay run in QuickBooks Online Core Payroll

by Intuit Updated 6 months ago

In this article, we'll walk you through the steps of deleting a pay run. We'll also explain what happens before and after the deletion, so you'll have a clear understanding of the entire process.

Before deleting a pay run:

  • You can delete individual payments within a pay run.
  • To correct an employee payment, make changes in the next pay run and the Full Payment Submission (FPS) will reflect the updates.
  • Print out payslips and reports for the pay run you want to delete, so you have all the necessary information when recreating it.

After deleting a pay run:

  • QuickBooks will attempt to delete corresponding journal entries, but it may not be possible if your books are closed. Check your journal entries to make sure the payments have been removed.
  • QuickBooks will delete the corresponding FPS, regardless of whether it was submitted to HMRC or not.
  • Employees who were assessed in the payroll will be reverted to their previous auto enrolment status. Contact your workplace pension provider and report accurate contribution amounts. Remember to print out workplace pension reports.
  • If you submit an EPS to notify HMRC for a tax period where no employees were paid for the period, QuickBooks will 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 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. The employee's P45 will be kept in their Documents. If no submission has been made yet, you can still edit the employee's leaver date.
  1. Go to Payroll and select Employees.
  2. Choose the Employee who needs their pay run deleted.
  3. Select the most recent pay period.
  4. On the Payroll Payment List tab, locate the pay run you want to delete and select Delete from the dropdown options.
  5. Select either to Delete this payroll payment or Close to cancel.
  6. Repeat these steps for any additional pay runs that you need to delete.

If you're having trouble deleting a previous pay run, it might be because of recent changes in your payroll. Here are a few reasons and solutions to try:

  • If you added a new pension, try deleting it first. If you can't do it yourself, don't worry! Reach out to support for help.
  • If you have employees who were recently added or assessed for an existing pension, make a note of their details and get in touch with support for more help.

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