The End of Financial (EOFY) year can be a stressful time of year for most businesses and organise the PAYG summaries for your employees only adds to the task that you and your payroll team need to perform. ClockOn has a number of step through wizards to help you with this process.

The following instructions with help guild you through the EOFY process within ClockOn. This guide will help you with Preparing your ClockOn Data ready for EOFY processing, Processing your last payroll for the financial year, how to Validate the data for the PAYG summaries, Create EMPDUPE01 file and PAYG summaries for the ATO and your employees. Plus a couple of other tips to help with finalising your payroll for the year.

NOTE: The PAYG Wizard is designed to act as a guide only. It is the Administrator's responsibility to determine how payment summaries are to be submitted to the Australian Taxation Office, that the values are correct and that all statutory regulations are complied with. Final figures produced via the PAYG Wizard should be independently verified.

The steps to process EOFY in ClockOn

  1. Processing the last payroll for the financial year
  2. Check your location details are correct
  3. Check the employee’s email address
  4. Adding any Reportable Fringe Benefits
  5. Validating data for the PAYG Summaries
  6. Creating the EMPDUPE01 file and PAYG Summaries
  7. Run the Single Touch Payroll (STP) wizard – Employee Update – Final Payroll
  8. Useful YTD Reconciliation Reports
  9. Finalizing the EOFY though to the ATO via STP

Processing the last payroll for the financial year

Before you perform any EOFY processing ensure that they process the last payroll of the year. If the pay period is in the current Financial year but the payment is going to be made in the new Financial year then you will need to tick the Process in New Financial Year tick box at the start of the last payroll of the financial year. This will put all the Year-to-Date (YTD) figures, from this pay run into the new financial year.

Preparing your Data for EOFY

To make running the PAYG summary wizard a little bit smoother please check the following:

1. Check your location details are correct

  1. To do this go to the Setup tab and click on Locations
  2. Double click on the location to open up the Location details
  3. On the Details tab ensure that the following details are correct:
    1. Company
    2. ABN
      NOTE: If this has been set incorrectly or there has been a change over the financial year please contact ClockOn support on how to resolve this.
    3. The Contact person’s Name who will be on the PAYG summaries
    4. Address details
    5. Phone and Fax numbers

3. Check the employee’s email address

Now is a good time to ensure that the email address for the employees is correct. If you are using the ClockOn Go App or the Web Portal you can advise the employees to make the change themselves (If this has been enabled). If you are needing to update this information you can do this by:

  1. Going to the Setup tab then click on Employee Details
  2. Select the employee that you need to updated the email address
  3. On the Personal Tab, updated the email address
  4. Click on Save

4. Adding any Reportable Fringe Benefits

Reportable fringe benefits need to be added into the YTD screen on the employee card file before starting the PAYG wizard. This is a Manual Addition to the YTD figures for each affected employees.

  1. To do this go to the Setup tab then click on Employee Details
  2. Select the employee that you need to add the reportable fringe benefits too.
  3. Go to the Pay tab
  4. Click on the YTD button
  5. Enter the amount into the RFBA (Reportable Fringe Benefits Amount) field
  6. Click on Save.

Validating data for the PAYG Summaries

Validation is required to be run before creating your EMPDUPE01 file and PAYG Summaries. This ensures that all of the employee details are valid and that they have payment details for the financial year. If you have Multiple locations that share the same ABN all of the employees in these locations will be consolidated for EOFY purposes

Some of the things that the validation checks

  • If an employee has had any financial payments for the year
  • The employee card files have correctly formatted TFN’s

Running the Validation Wizard

  1. Go to the Payroll tab and Click on Validate PAYG Summaries
  2. Select the location you are validating the data for. NOTE: you will need to run this for each location that has a difference ABN. 
  3. Select the Financial year. NOTE: It will default to the Latest available financial year.
  4. Click on Next
  5. You will be prompted with a screen showing all the valid employee (Ticked) and any employees with potential errors (Not ticked).
    1. If an employee is in error, double click on the error message and you will be taken to the area in ClockOn to make corrections.
      NOTE: All employees that you are required to report to the ATO on, for the financial year, need to be valid before proceeding. For example, the error message Group Cert Invalid:… means that the employee has had no income this financial year and is not required to be reported to the ATO. It is ok to leave this employee as unticked
    2. Once the issues are resolved the employee with have a valid tick against them.
  6. Click on Finish

TIP: Don’t forget to repeat this for each individual ABN

Creating the EMPDUPE01 file and PAYG Summaries

  1. Go to the Payroll tab and Click on Create PAYG Summaries.
  2. Select the LocationNOTE: you will need to run this for each location that has a difference ABN.
  3. Select the Financial Year EndingNOTE: Amendment is only required if you are resubmitting the EMPDUPE01 file to the ATO for the selected financial year.
  4. Click on Next.
  5. Step 1: Verify your location details. NOTE: If this is incorrect you will need to Close out of the Wizard and fix up in the location Manager (Steps above).
  6. Click on Next
  7. Step 2: Verify your contact name. This can be updated on this page.
  8. Click on Next
  9. Step 3: Employees to consider for YTD rebuilding. This screen will show any employees who have had manual changes made to their Employee YTD values and hence they no longer the same as what has been recorded at the time of payroll.
    You have the option to:
    1. Ignore all and this will use the current values in the employees YTD page
    2. Rebuild: this will amend the employees YTD figures to be was recorded at the time of payroll
    3. Restore: This is used after a rebuild has been completed for an employee and you wish to revert back to the manual changes that were made.
  10. Click on Next
  11. Step 4: Checks all the employees to see if they have any additional reportable super contributions above the current required minimum rate. This included Super Salary Sacrifice, Additional Employer Contributions (as established in the rule set).
    1. Click on the Calculate button to retrieve the employer contribution that is calculated at the end of payroll for the financial year. These will show on the RSEC Column after the calculate button is pressed
      NOTE: Manual changes to the employees YTD’s will show in the RSEC column, prior to pressing the calculate button, and will not be recalculated when you click on the calculate button. If you want to recalculate these figures to be what was processed at payroll, tick the include box and then the calculate button.
  12. Step 5: This is the list of employees that will be included in the creation of the file to be submitted to the ATO as well as your PAYG and ETP summaries.
    NOTE: Please untick any contractors that you may have on your books as they are not required to be in the EMPDUPE file
    1. Employees that are deselected are those that did not pass the validation check. to find out why or correct any employees you will need to cancel the wizard and re-run the validation wizard (as above)
    2. The Aggregate column advises of any employees who have 2 or more card files that share the same:
      1. Location ABN
      2. First and last name
      3. TFN
      4. Date of Birth
  13. Click on Next
  14. Select the file location of where you want to save your EMPDUPE01 file required to upload to the ATO. To do this click on the yellow folder icon and you will be prompted with a window to Choose a folder when where the EOFY data will be saved. By default, the file location will be in the ClockOn installation folder on your computer. When the file is created it will be created under a folder called EOFY/LocationName/FinacialYearEnding (example: C:\Program Files (x86)\ClockOn\EOFY\Malvern Entity 001\2018\EMPDUPE.A01)
  15. Click on Next
  16. Step 7: Printing the reports. On the final page of the wizard, you will have to option to Print and Email the Individual PAYG Summaries and ETP Summaries. For each type of summary, you will have the options to:
    1. Print all of the employee summaries.
    2. Print only the employee summaries who don’t have an email address in their card file
    3. Email all the employee summaries who have an email address in their card file.
      TIP: If you are unsure if you have any ETP summaries try printing them first before just emailing them.
  17. Click on Finish

TIP: You can run the Create PAYG Summaries wizard as many times as you need to check that all is reconciliation is correct. just be aware that by doing this the EMPDUPE01 file will be over written each time you run it. So the final time you run the wizard will be the one you upload to the ATO.

Useful YTD Reconciliation Reports

Below is a list of the useful reports that can be run if you require further reconciliation for the EOFY. Run all of the reports the Current Financial Year when selecting the periods. On the Superannuation report tick all of the Super Reporting Months that fit into the financial year.


PAYG Summary (YTD adjustments, compact)

This report will give you all the totals for the financial year and also show any YTD adjustments that have been made in the payroll.

Payroll Summaries – Payroll allowances/deductions (Adjustment Roll-up)

For this report select all of the allowances/deductions that are not included in the gross wages and are to be set as allowances on the PAYG summaries. You can then check the allowance amount and also 

Superannuation fund summary (Payment type)

This report will show you, by the Superannuation fund, the split of the employer contributions, super salary sacrifice and co-contribution amounts.

Finalizing the EOFY Through to the ATO via STP

Please refer to the link below for a guide on how to submit the EOFY values to the ATO via STP.

Single Touch Payroll (STP) - EOFY Submission