Bonus Payments


Bonus Payments (including Commission that is not included in every pay) are created by adding a pay line to the pay for an employee. This can be included in your regular pays. If you are decide to run a separate pay for bonus payments we highly recommend ensuring the period for the pay has already been covered by the regular pay cycle i.e. the end date of the bonus pay is no later than the end date of the most recent regular pay.  

There are different types of bonuses an employee might receive, which have different effects on the employee's holiday pay accruals, annual leave rate calculations, and tax calculations. The types of bonuses are:

Regular Bonus - the employee accrues holiday pay and the bonus will increase both the ordinary and average pay rates. 

One-off Bonus - the employee accrues holiday pay but the bonus will increase only the average pay rates. Use it for bonuses that occur less frequently than monthly, e.g. quarterly or annually. 

Discretionary Bonus - the employee does not accrue holiday pay and the rates are unaffected. A Christmas bonus is an example of this. 

To ensure that the holiday and tax calculations on bonuses are correct, it's important to use pay codes that are correctly set up to reflect the terms of the bonus.


This chart can help you decide which pay code you should use, and whether any special settings are required on the pay code you use:



Pay Codes

The first step is to ensure your pay codes are set up correctly under Setup > Pay Codes. To help with this, there are default Bonus pay codes set up in FlexiTime. The standard set-up is for there to be three pay codes available: Bonus - Regular, Bonus - One-off and Bonus - Discretionary. You can rename these bonuses to suit your requirements, or create new pay codes as needed. 

Some companies that have been using FlexiTime for a long time may have a single Bonus pay code. If this is the case you may need to change the pay code to meet your particular requirements. 

Bonus pay codes should be set up as a Taxable Allowance, with Units set to Other.

A one-off Bonus should have Exclude from Ordinary Earnings ticked.

A discretionary Bonus should have Exclude from Holiday Earnings ticked.


Spans Multiple Periods

Another consideration when paying bonuses is how the the tax will be calculated. When a bonus is included in every regular pay (for example a monthly salaried employee paid a monthly bonus in each pay) then the standard bonus pay code set up is adequate. If the bonus is paid on a different cycle to your regular pays then you need to edit the pay code and record how many months the bonus covers:



In this example it's a quarterly bonus, paid every three months. Another example would be a monthly bonus for employees who are usually paid weekly or fortnightly, in which case the Months should be set to 1.

You should also tick Spans Multiple Pay Periods if the bonus is paid on a different cycle to the standard pay, for example an employee paid monthly on the 1st of the month, receiving a monthly bonus paid on the 15th of the month. In this case the Months should be set to 1. 


Create the Pay

Once the pay code is set up appropriately, create the pay run for your employees and add it to the employee's pay. To do so, simply select the Pay Code dropdown in the top right corner of the pay, select the appropriate Bonus pay code and click Add

If you'd like to pay the bonus separately from the usual pay run,  you can create a new pay just for the bonus payment.  Set the Pay Date to the date that you'll be paying the employees and set the Start Date and Pay Frequency to be the same as the last wages pay for this employee.  This will ensure that the bonus is taxed correctly and that it won't affect the tax calculation in the next wages pay. 



Extra Pay

All Taxable Allowance pay codes provide some extra options: 


For a lump sum payment, tick Extra Pay. The chart above can help guide you on whether the bonus should be processed as an Extra Pay.

When Redundancy or Retiring Allowance is ticked there will be no ACC Earners' Levy applied to the tax calculation.  


What tax rate is used for a lump sum payment?

If Extra Pay is selected, FlexiTime will work out the employee's average pay for the last four weeks and gross this up, plus this pay amount, to calculate the employee's annual salary. This calculated annual salary is used to determine the tax rate to be used for this pay.  

For more information, please see the IRD's website.

Elected Lump Sum Tax (ELST) Rate can be used to select a higher tax rate to the calculated tax rate. If the calculated tax rate is higher than the ELST rate, the ELST rate will be ignored and the calculated tax rate will be used. 


For more details on how tax is calculated on bonuses, see the instructions at the IRD.


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  • Avatar
    Halfdan Hansen

    If an employee is eligible to get a bonus every month but only receives it 1/3 of the time - due to not meeting targets etc then should that Bonus when paid be a One-Off Bonus?


    Should Extra Pay be checked for One-Off Bonus' ?

  • Avatar
    Robert Owen

    Great question. Because the pay period of the bonus is monthly it should be treated as a Regular Bonus and included in Ordinary Earnings. You shouldn't check the Extra Pay box.

    One-Off bonus is confusingly named, the point being that it is a bonus paid less frequently than monthly and so shouldn't be included in Ordinary Earnings. Possibly periodic bonus would be a better name. Extra Pay should only be ticked for lump sum payments which include -

    * annual or special bonuses,

    * cashed-in annual leave,

    * retiring or redundancy payments,

    * payments for accepting restrictive covenants, exit inducement payments, gratuities, or back pay.