Jobkeeper Applications and Payroll Setup – Axis IT Consulting

Jobkeeper Applications and Payroll Setup

Started by Nathan Elcoate
April 20, 2020

JobKeeper Applications Now Open and Critical Payroll System Setup

Good Morning,


The ATO have today released the JobKeeper Applications via the ATO website

Access to the application will be via the ATO Business Portal and MyGov ID, hence please ensure you have first of all setup MyGov ID access to the ATO Business Portal.

If you haven’t yet set up a MyGov ID login, please see our past article for further information in that regard

Further in detail steps around the JobKeeper application process can be found in our previous article here

Once logged into the ATO JobKeeper Application, you will find the Enrolment Process under the Manage Employees menu, then click JobKeeper Enrol.

* Please note an enrolment form must be completed by each Employee, and returned to the Business for record-keeping purposes.

Next Click Enrol to commence the process. Please ensure you have read and understand the rules for applying for the JobKeeper Subsidy, and that your business meets the Eligibility Criteria.


The ATO have advised that the JobKeeper Subsidy will be run through and verified by the Single Touch Payroll system, digitally via your Payroll System. It will also work on set, pre-defined fortnight periods. It’s OK if your pay runs lapses these periods, as long you identify which period you began paying, and ended paying, the JobKeeper Allowance.

For this to work, a certain set of criteria have been established by the ATO, across all software payroll brands. You must label your payroll items specifically in sequence in order for the Subsidy (refund) to be triggered at the ATO end. Failure to do so, could result in lengthy phone calls to the ATO, or applications by your Accountant, to revise pay runs, and manually alter your Single Touch Payroll lodgements. This will delay your refunds.

The way the system has been designed is in fortnight numbers, these must be clearly labelled in your pay run, so that it corresponds with, and the ATO know, which pay run applies to which fortnight.

FN Dates Start allowance Finish Allowance
01 30/03/2020 – 12/04/2020 JOBKEEPER-START-FN01 JOBKEEPER-FINISH-FN01
02 13/04/2020 – 26/04/2020 JOBKEEPER-START-FN02 JOBKEEPER-FINISH-FN02
03 27/04/2020 – 10/05/2020 JOBKEEPER-START-FN03 JOBKEEPER-FINISH-FN03
04 11/05/2020 – 24/05/2020 JOBKEEPER-START-FN04 JOBKEEPER-FINISH-FN04
05 25/05/2020 – 07/06/2020 JOBKEEPER-START-FN05 JOBKEEPER-FINISH-FN05
06 08/06/2020 – 21/06/2020 JOBKEEPER-START-FN06 JOBKEEPER-FINISH-FN06
07 22/06/2020 – 05/07/2020 JOBKEEPER-START-FN07 JOBKEEPER-FINISH-FN07
08 06/07/2020 – 19/07/2020 JOBKEEPER-START-FN08 JOBKEEPER-FINISH-FN08
09 20/07/2020 – 02/08/2020 JOBKEEPER-START-FN09 JOBKEEPER-FINISH-FN09
10 03/08/2020 – 16/08/2020 JOBKEEPER-START-FN10 JOBKEEPER-FINISH-FN10
11 17/08/2020 – 30/08/2020 JOBKEEPER-START-FN11 JOBKEEPER-FINISH-FN11
12 31/08/2020 – 13/09/2020 JOBKEEPER-START-FN12 JOBKEEPER-FINISH-FN12
13 14/09/2020 – 27/09/2020 JOBKEEPER-START-FN13 JOBKEEPER-FINISH-FN13
Your first JobKeeper pay run would hence be JOBKEEPER-START-FN01 if you started the JobKeeper Allowance in the first period, and so on.

If you have an Employee end their relationship with you, then their pay run would be labelled JOBKEEPER-FINISH-FNXX where XX is the fortnight number they ended in.

This tells the ATO that this Employee no longer wishes to receive the JobKeeper Allowance from you.

Alternatively, where you are paying an Employee part wage, part JobKeeper Allowance, then that label would be JOBKEEPER-TOPUP. All Employees who are paid ONLY the JobKeeper Allowance will be paid as JOBKEEPER-TOPUP. After the initial payrun where you use JOBKEEPER-START-FNXX. Where XX is the fortnight number you have started in. 

Rather than go into full detail for each software Vendor, we have listed below the current guides for setup and management of JobKeeper Allowance, from each of the major software vendors in Australia.

Reckon Accounts:

MYOB AccountRight:

MYOB Essentials:

Intuit QuickBooks Online:



If you are not sure about any aspect of the JobKeeper Allowance enrolment process, or your Business’ eligibility for the allowance, please seek the assistance of your Accountant prior to making the application process.

We can, of course, assist via remote access to assist with system setup.

In all instances please refer to the ATO websites for guidance.



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