A regular pay run is how a business pays its employees on a schedule, such as every week, fortnight or month.

It is also possible to run ad hoc or unscheduled pay runs if required.

By default, you will have at least one pay calendar that was created when Deputy Payroll was set up. Your pay calendars group your employees into the various ways that they will be paid. Keep in mind that additional pay calendars can be set up anytime. 

• Prior to completing a pay run
• Accessing pay runs
• Processing a pay run
• Review the payslips
  • Summary tab
  • Payslips tab
  • Bulk Actions in a pay run
• Complete the pay run
  • Pay Your Team
• Pay run status
• Pay run FAQs

Prior to processing a regular pay run

Prior to processing a pay run, you should ensure that:

1. All employees payroll details are up to date including accurate pay rates assigned. This includes salaried employees.
2. All employees are assigned to their correct pay calendar. Note: some messaging in Deputy uses the terms, 'pay calendar' and 'pay cycle' interchangeably but they are referencing the same thing.
3. Default superannuation funds have been set up.
4. All recurring deductions, expenses and recurring extra earnings have been set up.
5. All timesheets that are to be processed in the pay run have been approved. Learn more about approving timesheets.

Accessing pay runs

Users with the access permissions of System Administrator or Payroll Administrator can access the Payrun page in Payroll.

Click on the Payroll tab and select Pay runs from the list on the left hand side.

In the main section of the page, you can see a tab showing Upcoming pay runs and a second tab showing Processed pay runs.

Note: there is also a button on the top right-hand side of the page to initiate an Ad hoc pay run. Read more about this option at Prepare an ad hoc or unscheduled pay run.

Let's look at the different columns on the Upcoming pay run page:

Trading

In the example below, where the business has multiple entities (ABNs) associated with the one business you are informed which entity the pay run is associated with by the Trading column. This column will not be displayed if you only have one entity (ABN) associated with your business.

Title

The name of your pay calendar (this was set when the pay calendar was created)

Pay Cycle

The frequency of pay assigned when the pay calendar was set up.

Pay Period

The dates for the pay period. The pay run will automatically include all approved timesheets in Deputy during this pay period.

Payment date

The date the payment for the pay run will be made. This date must be in the future by the time you complete you pay run in Deputy.

Staff

The number of employees assigned to this pay calendar.

Pay run status

Will display:

• Upcoming - if the current date is before the end date of the pay period 
• Ready - if the end date of the pay period has passed

If you have pay runs showing Ready you are ready to process your pay run.

Processing a pay run

Watch a short video for an overview of processing a pay run, or read below for more information:

Click Start on the right side of the page for the pay run you want to process.

A pop up will appear with the pay run details. 

Pay Cycle

The name you assigned to this pay calendar when you configured it

Year

The financial year this pay falls in. Most of the time you will be operating in the current calendar year but make sure you pay attention to this setting if you are doing a pay run to adjust for historical pays that may be outside the current financial year.

Run

This setting will default to the current pay period, but you can use the menu to select another pay period to process the pay run if required. Why is the pay run I want to process greyed out?

Birthdays

Any birthdays that fall within the pay period will be highlighted. This is of importance if a birthday triggers an age-related pay rate increase or age-related superannuation action for this employee, so please check you have the correct pay rates for this employee.

Payment date

The date the payment will be processed on. It is important to make sure this date is accurate now since all reporting will rely on this date as the pay date. It is also important that this date is a future date. If you set a payment date in the past and this is used to generate the ABA file then it is likely the bank will reject it. A date in the past may also impact your STP reporting obligations. 

Runs in the year (first pay run only)

The number of pay runs expected to fall in this financial year will be shown: 

• For weekly pay calendars, it could be 52 or 53
• For fortnightly pay calendars, it could be 26 or 27
• Semi monthly pay calendars will always be 24
• Monthly will always be 12 

For more information on how to manage financial years with 53 weeks or 27 fortnights, read our FAQs

Starting (first pay run only)

The day of the week the pay run starts on. Only relevant for weekly and fortnightly pay calendars. 

Once you have confirmed the information in the pop up, or made adjustments as needed, then click Pay run.

This will now process your pay run, but NOT complete it. This action will automatically retrieve all approved timesheets for employees assigned to this pay calendar in the pay period selected.

Review the payslips

Once a pay run has been processed, the next step is to review the team members' payslips generated in this pay run.

You will see the pay run has now moved to the Processed tab in Payruns and has the status of Processing.

Click View to start reviewing the payslips.

The next page you see is the Payslips page. If you need more screen space to focus on reviewing your payslips in this pay run, you can click the arrows to collapse either or both of the panels on the left.

There are two tabs you can use to review the payslips generated in the pay run:

Summary tab

On the Summary tab, you can see an overview of all the payslips in this pay run, with total hours and costs tallied. 

The difference arrows next to each of the figures can give you an idea of whether any amounts might be outliers from previous pay runs. 

Over time, as more pay runs are processed, the difference comparisons will become more useful.

You can click on Payslip on the right-hand side of the screen to view the details of any team member's payslip.

Payslips tab

The Payslips tab gives a more detailed summary of each team member's payslip.

The panel on the left lists each team member in the pay run and gives a summary of each team member's payslip. You can click on the team member's name to view their payslip or scroll down the region on the right to see all team payslips.

Read a more in-depth guide about the fields displayed in a payslip.

Review the payslips for each employee to ensure accuracy.

These are some of the things you might like to check or action:

• Pay rates and hours are correct - if you need to change these it is possible to do that directly in the payslip using the pencil button on the far right-hand side to edit. However, the recommended practice would be to unapprove the timesheet in Deputy, edit the timesheet, reapprove the timesheet then reprocess just the affected payslip(s) in this pay run.
• The employee has a super fund nominated (if eligible) - you can click on their name to go directly to the profile and enter super fund details if required. Click Reprocess to refresh the information in the payslip.
• Any relevant recurring expenses, deductions or extra earnings such as bonuses and allowances have been applied.
• If you need to add a one-off ad hoc deduction, expenses or extra earnings such as a bonus or allowance you can do that directly in the payslip.
• If you need to add a one-off ad hoc deduction, expenses or extra earnings such as a bonus or allowance to multiple payslips at once, you can use Bulk Actions.
• If you need to change the tax calculated, for example, you have applied a different method to a marginal tax calculation, it is possible to do that directly in the payslip using the pencil button on the far right-hand side to edit.
• If you need to change the superannuation calculation, the rate can be edited in the Employees Profile or Global Settings. If a payment should not attract Super, change the payment to the correct Class. 
   

Bulk Actions in a pay run

Actions you can execute on individual payslips, such as adding a deduction or reprocessing pay slip (and many more) can also be done in bulk to apply the action to individual pay slips or selected employees as required.

Click on Bulk Actions on the top right-hand side of the page (either Summary or Payslips tab).

Payment

If you select Payment from the Bulk Actions drop-down menu, you can select which employees you wish to apply the bulk action to using the check boxes on the left-hand side. Complete the details of the extra earnings payment, such as Bonus, and then click Add Payments.

The extra payments will be applied to the selected employees' payslips in this pay run only.

Leave

Select Leave from the Bulk Actions drop-down menu and then select a leave type. 

You can select which employees you wish to apply the bulk action to using the check boxes on the left-hand side.

Complete the details of the leave payment and then click Add Payments.

Expense

If you select Expense from the Bulk Actions drop-down menu, you can select which employees you wish to apply the bulk action to using the check boxes on the left-hand side. Complete the details of the expense, such as Super Sal Sac, and then click Add Expenses.

The expenses will be applied to the selected employees' payslips in this pay run only.

Deduction

If you select Deduction from the Bulk Actions drop-down menu, you can select which employees you wish to apply the bulk action to using the check boxes on the left-hand side. Complete the details of the deduction, such as Union fees, and then click Add Deductions.

The deductions will be applied to the selected employees' payslips in this pay run only.

Add Employee

If you select Add Employee from the Bulk Actions drop-down menu, you can select an employee to add them to the current Payrun.

This might be required if an employee was not active when the Payrun was processed. Only employees who are not currently in the Pay run are listed in the drop-down menu to select.

Once you have selected the employee from the drop-down menu, click Add Employee to the Pay run

Reprocess

If you need to reprocess to 'refresh' the payslips for ALL team members in the pay run after making any changes to:

• information in the employees' profiles or
• the employees' timesheets falling within this pay run
• payroll settings

select Bulk actions and then Reprocess.

You will see the following warning:

Any changes to the following areas will be reflected on the payslip:

• Timesheet
• Employee Profile
• Global Settings (Payroll settings)
• Payroll Rules (Recurring Deductions, expenses and extra payments)
• Groups (Pay calendars)

Any lines on the Payslip that have been modified will be recalculated.

Any lines manually added to the Payslip will remain.

Click I understand and then Confirm Reprocess Pay run

Delete Pay run

If you wish to delete an entire pay run, you can do this by selecting Bulk action, then Delete Pay run.

Note: only unlocked pay runs can be deleted and all pay run information will be removed permanently - this action CANNOT be undone.

You will see the following information about the Delete Pay run action.  Click I AGREE if you want to delete the pay run. You will then be asked a second time to CONFIRM the action.

The pay run will now be deleted and disappear from the Processed pay run list.

You can now start to process this pay run from the start again if you wish.

Complete the pay run

After confirming all payslip details are correct, click the Complete Pay run in the upper right of the page.

Pay Your Team

The Pay Your Team page will now be displayed so you can make all the payments captured in the pay run.

1. Confirm Payment Date

Confirm that your payment date is in the future and correct according to the date you want the bank to pay your team.

Use the date selector to set the correct date if necessary.

2. Create a back up

This is an optional step but downloading a copy of the pay slips allows you to keep a copy of the pay run for your own records. Click Download backup.

A file will download to your computer with a list of all the payslips in this pay run, similar to the example below.

3. Download the ABA file

Download the Australian Banking Association (ABA) file, which contains the net value of the payment for all employees in this pay run. It will also include any deductions and expenses that you have added a bank account to. 

Click Download ABA.

A file with extension .aba will download to your computer.

4. Upload the ABA file to your bank

Upload your downloaded ABA file to your supported banking portal to pay all your team members in one go.

5. Lock the Pay run

This is the final action within Deputy that will signal your pay run is complete.

Click Lock & Continue

This action will trigger the following:

•  
  •  
    • Lock the pay run
    • Payslips will become available to employees in the Deputy mobile application
    • Timesheets will be marked as paid
    • Leave balances will be updated in alignment with any leave timesheets.
    • You can no longer make any changes to the pay run.

Once the pay run is locked (this may take a few seconds) you will be automatically directed to Submit to ATO.

However, if you check the Pay Your Team page, the pay run now displays Unlock.

You can unlock the pay run to make changes or correct a mistake, however this should only be done if you have not uploaded the ABA file yet. If the ABA file has already been uploaded and you discover a mistake in the completed and locked pay run, it is best practice to leave the pay run locked and instead create a new ad hoc pay run to make the adjusted payments to correct for the mistake.

Note: Once you unlock the pay run it will revert to a draft state and employee will lose access to the payslips they previously had access to when you locked the pay run.

Once the pay run is completed and locked you are ready to submit the pay run information to the ATO via STP (Single Touch Payroll).

Note: You will need to manage when you submit the information to the ATO to meet your STP reporting obligations.

Pay run status

How do I know what stage I am up to in my pay run and what tasks I have left to do in a pay run?

Let's look at the various status messages we can see on the Pay run page to determine what state each pay run is in.

Upcoming Pay runs

There are two states a pay run can be in on the Upcoming pay run tab:

• Upcoming - the end date of the pay period has not passed yet - this pay run has not yet been processed
• Ready - if the end date of the pay period has passed, but the pay run is still in the ready state, this means the pay run has not been processed yet

Processed Pay runs

There are several states the pay run can be in on the Processed pay run tab:

• Processing - Pay run has been processed but not yet completed. The pay run is not yet locked and STP has not been lodged yet.
• STP Pending - Pay run has been processed and completed. The pay run is locked, but STP has not been lodged with ATO.
• STP Processing - Pay run has been processed and completed. The pay run is locked and STP has been lodged with ATO but ATO has not responded yet (STP submission can take up to 72 hours)
• STP failed - Pay run has been processed and completed. The pay run is locked and STP has been lodged with ATO but the submission failed. See Submitting the pay run to the ATO via STP 
• STP successful - Pay run has been processed and completed. The pay run is locked and STP has been lodged successfully with ATO
• Complete - The pay run has been processed and completed successfully with no errors from the ATO.

Pay run FAQs

Why is the pay run I want to select greyed out? 

When processing a new pay run and selecting a specific pay run you may see that some pay runs are greyed out and you can not select them. This means that pay run has already been completed and locked. 

Why do I see employees with $0.00 payslips? 

An employee with a $0.00 payslip amount generally means that they didn't have any timesheets, but the employees were a part of the selected pay calendar.

What happens if the payment data on the payslip is incorrect?

Your best practice action in this situation will depend on when you have realised the payment data is incorrect:

During payslip review and before you click Complete the pay run?

• Simply go to the employee's profile and update their details if they are incorrect or if the mistake is in the payment line go and unapprove the timesheet in Deputy, edit the timesheet, reapprove the timesheet then reprocess just the affected payslip(s) in this pay run.

After you have locked the pay run, but before you have uploaded the ABA file or submitted the information to the ATO?

• Unlock the pay run, then go to the employee's profile and update their details if they are incorrect or if the mistake is in the payment line, go and unapprove the timesheet in Deputy, edit the timesheet, reapprove the timesheet, then reprocess just the affected payslip(s) in this pay run.

After you have uploaded the ABA file to your bank or submitted the information to the ATO?

• In this instance, it is best practice to leave the pay run as it is and start an ad-hoc or unscheduled pay run to correct the mistake with readjustment payments.

How can I add leave payments that are not a part of a timesheet (such as salaried employees)?

You can add leave to pay runs manually by clicking the Add Leave on the employee's payslip and choosing the appropriate leave type. Please note that this is uncommon and leave will typically be handled in Deputy by the employee submitting a leave timesheet and that timesheet being approved using the normal approval process.

Can I add additional payments, such as bonuses, to pay runs?

Yes. You have two options here. You can:

• add deductions and expenses or extra payments such as bonuses and allowances as recurring payments which means they will automatically be added to a payslip whenever you process a pay run.
• add deductions, expenses and extra payments as a one-off ad hoc payment to a payslip.

How do I manage pay runs when I have 53 weeks or 27 fortnights in a payroll year?

In the New pay runs pop up, there is a field for managing when there are 53 weeks or 27 fortnights in a payroll year. This will occur if the first pay run of the year happens on or around the 1st of July.

The Australian Taxation Office (ATO) has an additional formula to add the extra tax required to the tax tables to avoid the possibility of a shortfall in Pay As You Go Withholding (PAYGW) for the employees. 

Deputy Payroll will automatically apply this additional formula based on the following:

• If the first pay run of the fiscal year falls on the 1st of July or the 2nd of July for leap years, based on payment date, there will be 53 weeks or 27 fortnights of pay runs, and this number will be preselected in the new pay run popup.
• If the Runs in a year setting is set to 53 weeks or 27 fortnights, that is then used to withhold more tax from the employee automatically as per the ATO formula.

Since this automatic application of the ATO formula ultimately results in more tax being withheld, it is important that businesses advise employees that the additional tax will be deducted as per the ATO's guidance, to avoid any possibility of a shortfall in tax withheld.

If you decide that you don't want Deputy Payroll to automatically withhold extra tax as per the ATO formula in 53 week or 27 fortnight financial year, then simply use the drop-down menu to adjust the setting in the pay run back to 52 weeks or 26 fortnights.

If your business takes this action to set the Runs in a year back to 52 weeks or 26 fortnights in a financial year where there are actually 53 weeks or 27 fortnights, it is expected that this issue will be managed externally by the business by adding additional tax on an individual employee basis where they receive the variation withholding request.