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Setting up automated pay schedules in QuickBooks Online Advanced Payroll

SOLVEDby QuickBooksQuickBooks Online Payroll2Updated March 21, 2022

Learn how to set up and schedule your payroll to run automatically in Advanced Payroll, so you can save time running payroll each payday–that’s one less thing for you to remember in your busy schedule.

You need to have completed your payroll setup and run your first payroll in order to set up pay schedules. To access your pay schedules in Advanced Payroll:

  1. Go to your Payroll Settings, then select Pay Schedules.

Step 1. Add a new pay schedule

  1. Select Add.
  2. Enter the pay schedule Name.
  3. Choose the Frequency to be weekly, fortnightly, monthly, four weekly, quarterly or annually. 
    • If you choose Monthly payment mode, this is where an employee has advanced standard work hours, the hours calculated in their pay may differ from month to month due to the number of days in the month the employee has worked. Use this if you want employee hours to be averaged over each month’s pay regardless of actual hours worked. Note that advanced standard work hours will still be applied for leave requests.
  4. Included employees. If you choose ‘Employees with timesheets in the following locations’, you must enter a location.
  5. Add a Payslip message. This message will show in the payslip message box on all pay runs for this pay schedule and on all employee payslips included in the pay run.

Step 2. Choose pay run warnings

In case of any errors, you can choose which pay run warnings and notifications that will stop the automated pay run when triggered. Select the pencil icon to see the full list of Pay run warnings. Understand what each pay run warning means here. 

You’ll need to manually finalise the pay run should a warning appear. Only the following warnings will cause an automated pay run to stop: 

  • Employee taking more leave than is accrued 
  • Employee with unpaid earnings 
  • Employee with negative earnings amount
  • Pending leave requests
  • Leave request extends past pay run dates 
  • Leave request ends before pay run dates 

Pay close attention to what warnings you do or don’t pick as this can impact the pay run, specifically warnings about leave and expense requests.

Step 3. Pay run finalisation options

You can set up the following preferences and apply it to all pay runs in a specific pay schedule:

  • Journals: This option will only appear if the business is connected to an online journal service and is set up in the Chart of Accounts. 
    • Select Export immediately to automatically post the payroll journal once the pay run is automatically finalised. Selected users will get an email notification if there are any issues. You can also 
    • Select Export journals manually to require the full access user to post the journal from within the pay run once the pay run is finalised.
    • You can also Export on a specific time and pay date. 
  • Submit pay run to HMRC: This can be immediately, manually or at a specific date and time. 
  • Publish payslips: This can be immediately, manually or at a specific date and time. 
  • Employee notifications: Choose to send or not send notification to employees.
  • PensionSync: This can be immediately, manually or at a specific date and time. 
  • Select Complete once you're happy with the finalisation summary.

Step 4. Pay run automation settings

Next, it’s time to choose what components of a pay run you want to automate. If you want to manually process the pay run from start to finish then you don’t need to change anything as manual processing is the default setting. 

  1. Schedule first pay run creation on: This field will pre-populate with today’s date and the upcoming hour (automated pay runs are scheduled on the hour), you can change the time and date by selecting the calendar icon.

Note: There may be a time delay depending on the size/volume of the pay run. For example, if you schedule the pay run to be run at 3pm, this does not mean the pay run will be finalised at 3pm. 

  1. Schedule last pay run creation: The default is Never, which means that there is no end date to automated pay run. Once you select On date, you’ll need to manually create the pay runs for this pay schedule after that date. 
  2. For initial pay period ending and With initial date period: If you have previously created pay runs for this pay schedule, the value that will appear here by default is the subsequent period end date of the last pay run created. If this is a newly created pay schedule or no pay runs have been created for this pay schedule, today's date will appear as the default value. Either way, you can always edit the date shown by selecting the calendar icon.
  3. Timesheet import: You can choose to either import timesheets for the current pay period, import all unpaid timesheets up to the current pay period or don’t import timesheets.
  4. Select Next.
  5. Select the warnings that will stop the processing of an automated pay run. 
  6. Select which users to notify via email when an automated pay run event occurs. Note: You can not add new users from here. Only users with full access permissions can access the affected pay run. 
  7. If you choose Finalise pay run immediately, you’ll see the following options: 
    • Journals: This option will only appear if the business is connected to an online journal service and is set up in the Chart of Accounts. 
      • Select Export immediately to automatically post the payroll journal once the pay run is automatically finalised. Selected users will get an email notification if there are any issues. You can also 
      • Select Export journals manually to require the full access user to post the journal from within the pay run once the pay run is finalised.
      • You can also Export on a specific time and pay date. 
    • Submit pay run to HMRC: This can be immediately, manually or at a specific date and time. 
    • Publish payslips: This can be immediately, manually or at a specific date and time. 
    • Employee notifications: Choose to send or not send notification to employees.
    • PensionSync: This can be immediately, manually or at a specific date and time. 
  8. Select Complete once you're happy with the finalisation summary.

Step 5. Turn on pay run approval

  1. If you select Yes in Do pay runs for this pay schedule require approval? you’ll need to choose the users to approve the pay run. If you need to, you can add and assign user permissions in your manage users settings
  2. Select Next.
  3. You can Edit the email message if you wish. 
  4. Select Next.
  5. If you want to, enter the number of days to send a reminder email if the pay run hasn’t been approved. 
  6. Select Complete.

How to stop an automated pay schedule

If you no longer want a pay schedule processed automatically, you can stop the automation at any time. 

  1. Go to your Payroll Settings, then select Pay Schedules.
  2. Choose the automated pay run you wish to stop. 
  3. If you want to stop and delete the pay run entirely, select Stop and then Delete. This will remove all automation settings and cannot be undone. 
  4. Don’t forget to Save.

How to pause an automated pay schedule

If you want to pause the automation of a pay schedule, say because you need to create a pay run for that pay schedule manually, go to: 

  1. Go to your Payroll Settings, then select Pay Schedules.
  2. Choose the automated pay run you wish to pause. 
  3. Select Pause. There will be no automated pay runs processed for that pay schedule while the pay schedule is paused. You’ll see there is now a Resume option in the pay schedule. You’ll need to select this when you’re ready to commence the automation again.
  4. Don’t forget to Save.

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