Employees can be assigned allowances to allow for additional payments or corrections to be done during the payroll process. These allowances on mass via Allowance & Deduction Manager, or individually from the can be applied individually through the Employee > Pay tab

This article contains information on the following allowance options.


  1. Adding Allowances
  2. Additional Advanced Options

Adding Allowances

To add a new allowance to an employee simply click the Add button on this screen.

This will create a new allowance item with the following default settings. 

From here you can assign the allowance a Name, Type, Amount, Payment frequency and a number of other settings to achieve the desired result, please see below for descriptions of each of the available options available when using the standard set of allowance options.

Please Note: This article contains an extensive listing of options avaliable, for simplicity sake we have provided a seperate article that contains a listing of commonly used examples for your convenience Allowance & Deduction Examples

Allowance Types

The following describes the different preset allowance types that can be set from the Type dropdown.


Provides a full range of options available for use within this screen.

Normal Allowance

This is the default option and lists the most commonly used option set for allowances.

Child Support (Garnishee)

Defaults the payment to be treated as a separate pay disbursement to a selected bank account, this is also reported as a unique type to the ATO.

Child Support (Deduction)

Defaults the payment to be treated as a separate pay disbursement to a selected bank account, this is also reported as a unique type to the ATO.

JobKeeper Allowance

Set the options required for the payments for the JobKeeper allowance program.

Employee Salary Sacrifice

Defaults the payment to be treated as a before-tax deduction, this is also reported as a unique type to the ATO.

Super Salary Sacrifice

Defaults the before-tax amount to be allocated to a superfund rather than the gross wage, this is also reported as a unique type to the ATO.

Super Co Contribution

Defaults the after-tax amount to be allocated to a superfund rather than the net wage, this is also reported as a unique type to the ATO.

Process As

The "Process As" option allows you to select how the payment or deduction will be treated at payroll.

Before Tax Allowance
Amounts added to increase the Before-tax wage within a period. 

Gross Tax Allowance

Similar to Before Tax Allowance, however, cannot be added to the super earnings base.

Before Tax Deduction
The reverse of the Before-tax allowance, in that it allows for amounts to be removed within a payroll, the amount needs to exist within the payroll prior to this point.

Tax Allowance/Rebate
Reduces the amount of tax the employee will be set to pay within the payroll.

Additional Tax
Increases the amount of tax the employee will be set to pay within the payroll.

After Tax Allowance
Grants an additional amount to the employee's net wage. 

After Tax Deduction
Deducts an amount from the employee's net wage. 

Reimbursement GST Inclusive: 
Are employee purchases on behalf of the company, such as stationery.

Reimbursement GST Only: 
Are for the GST component only.  Mostly used for contractors.

Reimbursement GST Exclusive: 
Are employee purchases such as fresh fruit for staff breakfast.

Pay Disbursement
Allows the user to allocate a portion of the employee's net wage to a separate bank account.

PAYG Location

The PAYG Location indicates how the allowance will be treated when processed through to the ATO.

Gross Salary & Wages

This is the most common and therefore the default option and will allocate the allowance amounts to the employee's gross wage.


This PAYG type allows for the assigning of the amounts to be reported to the ATO outside of the gross wage amount.

When this option is set you will also be required to set a corresponding STP Type

  • Award Transport Payments
  • Bonus and Commissions
  •  Cents per KM
  • Directors Fees
  • Laundry
  • Overtime Meal
  • Qualifications/Certificates
  • Other
  • Tasks
  • Tools
  • Travel
  • Fees
  • Workplace Giving

If you are unsure as to if you need to process your allowance in this way please contact the ATO or your governing body for advice.

Union Fees

Allocates the allowance amount paid to union fees to the ATO.


Allocates the allowance amount paid to Community Development Employment Projects (CDEP) to the ATO.


The amount fields allow you to specify how the amount is to be allocated as well as the total and payment frequency within the payroll.

Employee Base Rate

Uses the employee's hourly rate as defined on the pay tab within the employee details screen.


This is the default value and uses a customizable amount (defined on the field to the right of this)

Minimum Rate

Compares the employee's base rate vs any special rates for the affected timesheets and uses the lowest pay rate available. 

Percentage Of Wage

Pays the allowance based on a percentage of the employee's current payroll wage.


This option can be used to indicate the frequency of the payment, whether it is to be applied on a weekly, fortnightly, monthly, or on a per-payroll period basis. 


The Cost option allows the user to indicate where they want the payroll costings to be allocated for the allowance, whether it be based on the employee's default location, based on where the employee worked (timesheets) or based on department cost splits.


The Options dropdown allows for additional settings for how the payment will be treated at payroll. These options will be disabled/enabled depending on the chosen Process Type.


Bonus Payment

This field is used to indicate that an amount is a bonus payment for internal reporting without allocating it to the PAYG Allowance type. This is only valid for internal ClockOn reporting.

Display Allowance Name in E.F.T

This option is used for the "Pay Disbursement" process as type. and allows for the amount to be identified easily on the bank file once submitted to the bank. 

Include in Payroll Tax

Determines whether the amount will be considered for the Payroll Tax calculation.

Include Paid Breaks

This only affects the allowance created when using the Per types that require timesheets.

Pay In Next Pay Only

Automatically reduces the amount for the allowance to 0 after the pay run, this is useful to prevent accidental overpayment from one-off adjustments. 

Include/Exclude in Super Earnings Base

Determines whether or not the allowance amount should be considered for the super calculations.

Export Options

This provides an area where you can allocate the allowance a journal code, to allow it to be allocated to a specific account in your accounting system.  

Additional Advanced Options

If the Type is set to Generic then the user will be presented with several more options for processing the allowance, please see below;


This allows for advanced triggering for the allowance for items such as if they worked more or less time for a shift, they work excessive overtime, they work a set number of hours past their shift end, or if they have split shifts within a single period.


Allows for the allowance to be selectivly called on specific days of the week.


Allows the allowance to be paid if the employee worked either before, after or between a specified time range.