Getting Started
  Your Business Settings
  Export From Other Systems
  Add An Employee
  Clocking Hours
  Timesheet Software
  Grouping Employees
  Management Configuration

  The Roster Process
  Roster Templates
  Roster Calendar
  Calendar View
  SMS Rosters

  The Timesheet Process
  Timesheet vs Roster
  Timesheet from Roster

  The Payroll Process
  A Payrun
  Leave and Public Holidays
  Rate Rules
  Shift Rules
  Break Rules
  Deduction Rules
  Extra Rules
  Time In Lieu
  Worked Public Holidays
  Jobs and Cost Centres

  The Leave Request Process
  Leave Request Review
  Leave Payroll Process
  Skills Matrix

  Single Touch Payroll
  Payment Summary
  Xero Integration
  MYOB Integration

Other features

  Processing Super

SuperChoice (Old process)
  Super Clearing House
  SuperChoice Setup
  Adding Super Fund
  Adding Employees
  Super Payment

  Employee Console
  Smartphone Login
  Push Notification
  Requesting Leave

  Partner Logo
  API Hello World
  API Employee
  API Timesheet
  API Payroll
  API Jobs
  API Roster

  Data Security
  Privacy Policy
  Terms Of Use

  Print Guide

Processing a Payrun

Each periods payroll must be processed, this guide will go through the process that your payroll officer will perform.


Menu > Payroll > Payruns


Once all timesheet data has been checked or approved, you can start your payrun.

Click New Payrun to start a new run.

Start Payrun

Most of the values to start a payrun should be correct.

You just need to fill the payment date.

Mouseover the info dots to learn more about each field.

If it's your first run in Microkeeper, you will need to select the run you want to process for.

If it's your first payrun for the financial year, double check the number of runs that are expected for the year is correct.

Microkeeper will predict how many runs are likely based on your payment date in arrears value.

Starting calculations

When you begin your Payrun, the timesheet data is converted into payroll data.

All the rules you have created are applied in relation to the timesheet data including overtime penalties, unpaid breaks etc.

Employee entitlements which include personal leave, annual leave, long service leave and/or rostered days off are calculated and accrued.

Super is calculated based on the employee's settings.

Tax is deducted using the current tax tables.

Completed calculations

View payslips for payrun

After the calculations are complete, a line will be added to the payrun feed.

If you need to run the payrun again for all staff you can click the grey Payrun button.

If you need to run the payrun again for an individual, which is usually recommended, there is a Payrun button on the individual's payslip.

To view the payslips for that run, click the grey Payslip button.


From the payslip page, you can view each individual payslip.

You are able to add leave to the payrun and any extras or deductions that apply to the payrun.

You should only need to add extras or deductions if there are no rules in place for the payment.

If you find you are adding the same extras or deductions every payrun, you may need to review your payroll rules.

Add Amendments to Payroll


To bulk add a payment such as an Incentive or Bonus click the Payment Button.

Other bulk payments

From this page you can

  • Select employees that the payment applies to
  • Add payment description 
  • Add the rate and multiplier
  • Select the payment classification
  • Import a CSV of Payments to be uploaded, the format of which matches column order in the above screenshot

Once you have entered in the relevant details click Add Payments

The details entered here will be automatically applied to the individual payslips.

To leave the page, click Back to Payslip

Confirmation message

Other Payments from a file

To add payments from a file, for example, Salary Packaging.  

Start by clicking the Add Payment button on the Payslip, then click Upload CSV File. 

Select a CSV File in the below column format and once uploaded it will fill the below fields with the details of the file. 

Employee Name, Description, Job, Rate, Hours, Multiplier, Classification, STP class.

Applying Leave

Both worked and unworked leave will automatically appear on the payslip.

For unworked leave please review the Leave and Public Holidays guide.

For worked leave please review the Worked Public Holidays guide.

Editing a Payslip

You can check and add on any entitlements or make changes to any of the calculated data on the Payslip.

Below is an example of a Payslip, on the right you can add, edit or delete any of the lines.

Payslip changes adjustments


You may, on an occasion such as termination, be required to pay out any outstanding leave balances.

To do this, you need to select Final located at the top of the payslip. 

A screen will pop up auto-populated with data for the employee.

You have the option to payout Long Service Leave.

Click Terminate to calculate their final payout. 

Check to ensure the payslip is correct and the Annual Leave balance is now zero. 

A Separation Certificate may be required for terminated employee's receiving Centrelink Benefits.  

Payroll Completion

Once the payroll data is accurate, and the payment date is correct, an .ABA file can be generated.

Payslip back up aba lock week

You can then save the payslips to a PDF back up, print payslips and Lock the Payrun, making payslips available to your employees online.

After locking the payrun you will be able to lodge the Single Touch Payroll Form.

STP Lodging  will be available from 1st of July 2018

For more information about Single Touch Payroll

 Please note, any changes to Payroll Rules must be confirmed by the delegated Payroll Officer.