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Set up pay run warnings in QuickBooks Online Advanced Payroll

SOLVEDby QuickBooksQuickBooks Online Payroll5Updated March 29, 2022

Depending on how you set up your pay run warnings in Advanced Payroll, warnings could appear as soon as a pay run is created or during the pay run. Here's how you can set it up in QuickBooks, plus understand what each warning means.

If you see a warning while creating or running a pay run, select the Warning to expand the details and get more information.

How to set up warning for a pay run

You can choose which warnings display for a certain pay schedule in your QuickBooks. To set this up, all you need to do is:

  1. Go to your Payroll Settings, and select Pay Schedules.
  2. Select the pay schedule you want to set up warnings for.
  3. Select the pencil icon next to pay run warnings to open the list of warnings which you can choose from.
  4. Tick warnings you would like to appear on pay run. Alternatively, you can untick the warnings you want to stop displaying on pay runs for this pay schedule.
  5. Select the X to close the Pay run warnings window.
  6. Select Save.

List of pay run warnings and what they mean

Select the pay run warning to reveal more information.

You will not be able to generate a payment file for the pay run as BACS Details have not been provided (Note: If you don't want to generate a payment file, you can ignore this warning).

This is displayed when an employee is attempting to take more leave than they have accrued.

This is displayed when an employee has a birthday during the pay run period and therefore may need to have their rate of pay reviewed.

This is displayed when the anniversary of the employees start date occurs during the pay run period and therefore may need to have their rate of pay reviewed.

This will be displayed when the net payment amount for an employee is less than 0.

This is displayed when an inactive employee who has previously been terminated appears in the pay run.

This is displayed when a previously terminated employee, who is still owed an expense reimbursement amount from their expense pay run inclusion, appears in the pay run.

This is displayed when an employee's qualification has expired within the pay run period.

This is displayed when there is more than one earnings line associated with the same timesheet line that contains the same units, pay rate, total earnings and note.

This is displayed when an expense has been applied in a pay run and does not contain a tax code. This is only applicable where a business is connected to on online journal service and has synced their tax codes against the expense categories.

This will be displayed for any employee whose leave entitlement has reached the maximum accrual for the year. For example, say an employee is entitled to 'Special Leave' and the maximum accrual entitlement for this leave is 10 hours per year. When the employee reaches the accrual and now has a balance of 10 hours for the leave year, this warning will appear.

This is where an employees auto enrolment status has changed.

If the employee has had a refund from the pension contribution.

Either the user hasn't authorised the scheme with the pension provider in PensionSync, or the authorisation details have been changed and the user needs to re-authorise using the new credentials to make a submission.

The employee has had a tax code updated and applied to the pay run.

The system hasn't been able to apply a tax code update. The error message should explain what's wrong, for example the tax code could not be applied due to an unauthorised EmpRef so the error would need to be fixed to stop it from happening again.

This is displayed when the employee's National Insurance (NI) has not been provided.

The system is calculating a part payment either due to employee leaving or starting part way through a pay run.

This is displayed if an employee has not earned above the National Minimum Wage/National Living Wage.

The late submission is when you are sending in the FPS (Full Payment Submission) file late, so after the pay date. This could happen because you need to correct YTD figures, or you have had to pay an employee something that has been missed. You need to select a reason (they are listed in a dropdown box) as to why you are sending a late submission of the FPS file, otherwise HMRC will automatically apply a penalty.

This is displayed when an employee has submitted a leave request pertaining to any dates within that pay period, that is yet to be approved. Pending leave requests cannot be applied in the pay run unless approved. Additionally, for automated pay runs, pending leave requests will not be automatically applied in the pay run.

This is displayed when an employee's leave request dates back in the past and is therefore relevant to previous pay periods.This warning is important as it highlights only a portion of the leave request should be applied in the pay run.

This is displayed when tasks have been created but not completed for the pay run in question.

This is displayed when an employee has submitted an expense request pertaining to that pay period that is yet to be approved. Pending expense requests will not be processed in the pay run unless approved. Additionally, for automated pay runs, pending expense requests will not be automatically processed in the pay run.

This will be displayed when an employee has an earnings line with hours applied, but the total value of the earnings line is 0. This usually indicates there's an error with the employee's rate of pay.

A P9 is issued by HMRC between February and the start of the tax year to inform you of specific tax codes changes. These should not be applied until the pay runs are in the new tax year. Note: The system will automatically check for any changes.

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