Payroll Guru - End of Financial Year (EOFY) - Single Touch Payroll (STP)


PLEASE NOTE - - PG is decommissioned. When PG was decommissioned all clients were asked to do their final STP payfile to close out whatever of the financial year they had done in PG before moving to their new payroll system. There is no option to do any STP or final payfiles with PG anymore as we are no longer connected to the ATO. If there's anything you need to report to the ATO - it will need to be done manually. You'll have to contact the ATO and ask how they would like you to get the data to them.




1) Updating YTD Values
      a. Set up of allowances

2) Checking STP submitted data & making changes in PG for EOFY STP submission. 
      a. Generate a PAYG summary report
      b. Changing any previously submitted STP information
      c. Adding any extra information i.e.  fringe benefit payment (FBT), lump sum payments, termination payment deductions

     d. Gross, RESC, Salary sacrifice 

3) Re-generating and reviewing the PAYG Summary

4) Process the Final STP EOFY Payrun

5) Submission of EOFY data to ATO

6) Other Information


EOFY is important with respect to STP submission to the ATO. The ATO guide on final STP Payfile submission can be found here:

The final STP payfile submission allows an employer to make an official declaration to the ATO that they have provided all the information for each payee for a financial year. 

This declaration allows the ATO to make the payee information available and authorised for use for income tax return prefill for employees - and it extinguishes the payers liability to provide a payment summary for that payee.

Upon submission of the final STP payfile, employers have a final opportunity to add extra information (that was not able to be submitted in payfiles i.e. FBT), and cross check against submitted details to see if any discrepancies need to be corrected. 


  • Final STP payfiles need to be submitted to the ATO by 14 July 2020
    • If you need more time, you can apply for an extended due date to make your finalisation declaration.
  • Once a final STP payfile has been submitted you can amend it:
    • Please contact us if you are needing to amend final figures transmitted to the ATO.
    • If you need to amend details after making a finalisation declaration, you should submit these as soon as possible. We also recommend that you notify your employee of the any changes to their finalised income statement. 
  • An employee will be able to see an “AUTHORISED FOR TAX RETURN USE” once the STP data has been verified by the employer through the submission of the final STP payfile.
    • Until such time the employee will see a message in the portal saying the data is not finalised and not ready for use.


1) Updating YTD Values

If YTD leave, base and/or allowance values need to be updated, these can be updated by following the guide:

Payroll Guru - configuring YTD values

a. IMPORTANT - Set up of Allowances 

If you chose to allocate allowances to not appear in Gross amounts then it will be reported separately to the ATO through STP.  If you need to change this to have it included in Gross - you need to change this before your final STP payfile submission.


- The below image depicting allowance handling is an example only.

- Please check the ATO guide or with your payroll advisor for guidelines related to the correct way of handling allowances. 




2) Checking STP submitted data & making changes in PG for EOFY STP submission. 

a. Generate a PAYG summary report

  • Click on “Reports” -> PAYG Summaries
    • if an employee is missed on this, their final payfile will not be reported to ATO for this FY i.e employee had no normal payruns in the FY and just had FBT, lump sum, or termination payment paid out - the user will not be part of the report.
  • “Include” all employees. 
  • Select the financial year and submit
  • Click "View Summary Report for 2020"
  • Click “create PAYGPS Report”
  • Select all employees
  • Click “create PAYGPS Report”



  • This will generate the below PAYG summary main page 
  • Click on “View Summary Report” to see PAYG summary report. 
    • This is where you can check all data submitted from Payroll Guru to the ATO. 



b. If you need to change any previously submitted STP information

If you need to change any previously submitted information this needs to be done through ad hoc payruns done BEFORE the final STP payfile submission.

An ad hoc payrun can be done to add or subtract (negative payments) amounts. If you are required to do this please email and let us know what you are trying to achieve and what you are planning to do - and we can double check your process for you.

c. If you need to add any extra information i.e.  fringe benefit payment (FBT), lump sum payments, termination payment and deductions.

To add FBT (which can not be added until the final STP payfile) or add any other lump sum payments or deductions you must run an AD HOC payrun.

  1. Create a new ad hoc payrun
  2. Add the employees to it that you need to add payments or deductions to.
  3. Add a $0 adjustment line e.e. add a pay code adjustment $0 and then add greater than 1 hours/unit.
  4. Add the information into the employees payslip - by clicking on the "STP Details" link beside their name.


  5. Enter the required values in the following screen ensuring the "Add Record" or "Save" buttons are used 


   6. Process the pay run as normal


d. Gross, RESC, Salary sacrifice 

Definition of Gross Payment

  • Report Guidance: 
    • The year to date gross payment includes all salary, wages, bonuses and commissions paid to a payee, company director or office holder.  Do not include amounts reported separately in total allowances, Lump sum payments, CDEP, RESC or Exempt foreign employment income.  Refer to the STP Business Implementation Guide for a list of all payments must not be reported.  Do not include amounts that have been salary sacrificed.
    • If you need to report CDEP, exempt FEI or INB PAYGW for a payee but no YTD Gross payment exists, record zero for this field.
  • Business Definition: 
    • The amount paid to an employee, company director or office holder in the form of salary, wages, bonuses and commissions.
  • Business Guidance:
    • Gross payments also include: pensions and annuities; compensation, and sickness or accident pay. 
    • Allowances you paid to compensate for specific working conditions and payments for special qualifications or extended hours 
    • Allowances you paid to cover expenses that are not tax deductible to the payee - for example, normal home-to-work transport expenses  
    • Holiday pay or bonuses, and - amounts you paid for unused long service leave, unused holiday pay and other leave-related payments that accrued after 17 August 1993, except if the amount was paid because the payee ceased employment under an approved early retirement scheme, invalidity or bona fide redundancy
    • Include all salary, wages, bonuses and commissions paid to the payee as an employee, company director or office holder.  
    • Include the total gross amount before amounts are withheld.
    • Also include the following amounts: 


  • Do not include amounts that have been salary sacrificed.



Reportable super (RESC)

  • In the Message Structure Tables the super area has two items for super amounts:
    • This is the value, during the relevant period, for employer superannuation contributions that are additional to the compulsory contributions where the employee influenced the rate or amount of contribution.
    • Contributions made by the employer for an employee in respect of an income year where ALL of the following apply:
      • The superannuation guarantee law.
      • An industrial agreement.
      • The trust deed or governing rules of a super fund.
      • A federal, state or territory law.
      • The employee influenced the rate or amount of super the employer contributed for them
      • The contributions are additional to the compulsory contributions employer must make under any of the following
    • This is the year to date value of Reportable Employer Super Contributions.  Report throughout the financial year or when available.  Refer to the STP Business Implementation Guide for detailed instructions on reporting.
    • (1) Super guarantee (9.5%)
    • (2) Reportable super (RESC) 

How to report RESC in PG:

  • Enter RESC against Payslip


  • Confirm RESC in PAYG Summary



How to update Salary Sacrifice 

  • Go to “Company” and then to “YTD Summary”
  • Update the “Super Sacrifice” section.



Confirmation Salary sacrifice is not included in Gross

    • Any amount in salary sacrifice will not be included in Gross.
      • If the YTD salary sacrifice amount is updated then the Gross value will be changed in PAYG Summary 
      • The gross value will be changed in STP and reported to ATO
      • Salary sacrifice figure is not reported to ATO separately


Example below: Employee with RESC 500


Example Below: Payg summary with Gross, RESC, Salary sacrifice


3) Re-generating and reviewing the PAYG Summary


Once the employer/user has added or amended anything required and sent the data to the ATO via their adhoc payruns - a PAYG summary report needs to be re-generated and checked. This shows what has been submitted for the current FY for each employee.  

NOTE: Please wait until after the ATO has sent a “successful” response to any adhocs payruns you have been required to submit, before you run this report, otherwise the data will not have had time to have been processed by the ATO.

  • Follow the steps in 1 (a) to generate the FY PAYG Summary.
  • Check the report.


4) Process the Final STP EOFY Payrun


Once the PAYG Summary report has been run and all the figures have been checked and are accurate, the next steps can be done. The PAYG summary report will be used as the basis for the data that will be submitted as an EOFY $0 payrun - so it’s important the report has already been checked and verified.


  • Go to Payrun -> Create new payrun -> Change date to be within the FY you are wanting to finalise for -> Click the checkbox “EOFY” -> click on “set dates”
    • NOTE: When you check the EOFY option you are declaring that the data is correct and that it’s suitable to be submitted as your final STP payfile (there are ways to resubmit final payfiles within 14 days if required)

  • Click “set dates”.
    • NOTE: Once you click “set dates” Payroll Guru will automatically define and process a $0 pay run which will include all employees that you have selected to be part of the FY. 


  • You will end up with a payrun screen like the one below. 
    • This means the payrun has been processed.
    • Once the final STP payfile has been successfully accepted by the ATO it will show up in the STP status of the payrun.



5) Submission of EOFY data to ATO

EOFY data will be submitted to ATO as per existing STP process. The payrun status will be updated in the payrun details page.

6) Other Information


Non-STP Reporting

If you have made payments to employees that haven’t been reported through Single Touch Payroll, you’ll need to send a payment summary to each of these employees and let the ATO know by lodging an annual report.

This tax time, you’ll need to order any paper forms using the ATOs online ordering service at

You can find more information on which forms to complete and how to order them at


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