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Delete a pay run in QuickBooks Core Payroll

by Intuit•44• Updated 1 month ago

Learn more about when and how to delete a pay run in QuickBooks Core Payroll. We’ll explain what happens before and after deletion, outline common scenarios where you might need to roll back payroll, and walk you through the steps to delete a pay run successfully.

This article is for customers who use QuickBooks Core Payroll. If you’re using QuickBooks Standard Payroll, follow these steps instead.

Before you delete a pay run

Before removing a pay run, make sure you’ve taken the necessary steps to save any important information. This can help prevent data loss or confusion when recreating the payroll.

You can delete individual payments within a pay run if you don’t need to remove the entire run.
If you need to correct an employee’s payment, you can usually do this in the next pay run. The Full Payment Submission (FPS) will reflect the updates.
Print any payslips or payroll reports for your records, as they won’t be available once the pay run is deleted.

What happens after deleting a pay run

Deleting a pay run can affect journal entries, pension settings, and HMRC submissions.

Here's what to expect

QuickBooks will attempt to delete any related journal entries. However, if your books are closed, this might not be possible. Check your journal entries afterwards to ensure they reflect the change.
The FPS associated with the pay run will be deleted, even if it’s already been submitted to HMRC.
Auto enrolment statuses will revert for employees assessed during the deleted pay run. You may need to contact your pension provider to report accurate contributions and reissue workplace pension reports.
If an EPS was filed for a period with no employee payments, deleting the pay run will also delete the EPS. You’ll be prompted to create a corrected submission.

If the pay run included a leaver and an FPS was submitted, the employee’s leave date becomes locked. Their P45 remains in their Documents. If no FPS was submitted, the leave date can still be edited.

How to delete a pay run

Follow these steps to delete a pay run.

To delete a pay run

Go to Payroll and select Employees.
Choose the employee whose pay run you want to delete.
Select the relevant pay period.
Under the Payroll Payment List tab, find the pay run and select Delete from the dropdown menu.
Select Delete this payroll payment, or Close to cancel.
Repeat the steps for any additional pay runs you need to remove.

Troubleshooting: When and why to delete or roll back a pay run

There are a few common reasons why you might need to delete or roll back a pay run. Here’s when it’s appropriate — and what to do:

You’ve made a mistake in a recent or past pay run

If you’ve noticed an error in a pay run you just submitted (or in a previous one), you may need to delete or roll back the payroll to the period in question.

Always roll back from the newest to the oldest period if multiple corrections are needed.
Once you’ve made your corrections, you must resubmit the FPS to HMRC for the corrected pay run.

Something was missed from a previous pay run (e.g. SSP not added)

If statutory pay or another adjustment was missed in a past period, it might not be appropriate to fix it in the current pay run.

Delete or roll back the original pay run, make the changes, and reprocess it.
As above, be sure to resubmit the corrected FPS to HMRC.

Still can’t delete the pay run?

If you’re having trouble deleting a pay run, it could be due to recent changes in your payroll setup:

New pension scheme added? Try deleting it first. If you’re unable to do this yourself, contact support for assistance.
Employees recently assessed for an existing pension? Make a note of their details and reach out to support for guidance.

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