Payroll Guru - end of financial year


PLEASE NOTE: Given the introduction of STP and Payroll Guru's new guidelines for reporting via STP in November 2019, this EOFY article is now superseded. New EOFY guidelines for the end of financial year 19/20 will be released in April 2020. 


This article includes the following topics:

  • ATO contact details
  • PAYGPS lump sum values
  • Updating YTD values
  • Updating PAYGPS allowance values
  • Summary report
  • Creating the EMPDUPE file from Payroll Guru
  • Submitting the EMPDUPE file to the ATO
  • Email PAYG Summaries
  • Creating PAYG summary archive

ATO contact details

For any enquiries in regards to the ATO ECI Client please contact the ATO for support.  Their contact details can be found here (

NOTE: Before processing the EMPDUPE file and PAYG payment summaries, you should ensure that your payroll data in Payroll Guru matches the general ledger in your accounting system (wages, superannuation and PAYG). If discrepancy are found, ensure all journals have been entered correctly and if in doubt, speak to your accountant/advisor.


PAYGPS lump sum values

If there are any PAYGPS lump sum values, these need to be added into the PAYGPS lump sum values section of Payroll Guru.

1. Open Payroll Guru

2. Click company

3. Click PAYGPS Lump Sums

4. Select the financial year

5. Enter the values and update


Updating YTD values

If YTD values need to be updated, these can be updated by following the guide here:

Payroll Guru - configuring YTD values


Updating PAYGPS allowance values

Allowances may need to be handled specific ways on the PAYGPS.   Before producing the PAYG summaries these need to be checked:

1. Click Reports

2. Click PAYG Summaries

3. Click "Allowance Setup"

4. Follow the instructions to set the options Include in PAYGPS, Include in Gross Wages and List Allowance separately if they apply to the allowance.

Refer to the ATO help centre or your accountant if unsure.


Summary report

The PAYGPS report should be used to balance against your accounting system to identify any discrepancies

1. Click reports

2. Click PAYG Summaries

3. Click "View Summary Report .." and follow the prompts

The ATO requires that values on the PAYG summaries to be rounded down to the whole dollar.  Please ensure you are taking this into consideration when auditing and balancing. 


Creating the EMPDUPE file from Payroll Guru

1. Open Payroll Guru and login to your account

2. If you have access to more than one organisation, choose the correct organisation

3. Click Company then EMPDUPE Files


4. Select Create or Recreate depending on if the file has already been created:

5. Select the employees to include and if you are producing an amendment file, this can be selected also

6. Click create file and once the file has been created, the screen will refresh and you will see Download - 

If you receive any errors producing the file please provide a screenshot showing the error.

 7. Right click Download and click Save link as or Save target as depending on your browser:


8. Download the file to your computer


Submitting the EMPDUPE file to the ATO

Once you have obtained the EMPDUPE file, you can submit through the ATO online portal located HERE.

If in doubt, please speak to the ATO.


Email PAYG Summaries

Once the EMPDUPE file has been submitted:

1. Open Payroll Guru and login to your account

2. If you have access to more than one organisation, choose the correct organisation

3. Click Reports -> PAYG Summaries

4. Choose the correct period ending and click Submit

5. Click Send YEAR PAYG Summaries

6. A list of employees will be displayed (employee names have been removed from this example)


8. Check all employees you would like to send PAYG summaries to, and click Send PAYG Summaries

9. PAYG Summaries will be emailed to all employees selected. 

Note: if you see

X PAYG summary set to send to Payroll Guru - PAYG summaries have NOT sent to employees

X PAYG summary set to send to employees - PAYG summaries have been sent to employees 


PAYG summary archive

A PAYG summary archive can be created by clicking the Create YYYY PAYGPS Archive button:


Then following the prompts. 

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