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.

New Payrun Configuration

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.

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.

A standard payslip


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.


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

Bulk Amendment Options

Example of Bulk Import Payments

From this page you can

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.


An employee can be terminated through the Payrun process. 

Click the Final button on the employee Payslip. 

Final button on an employees payslip

The One Tap Terminate window will open. 

The One Tap Terminate window and settings

Configure the options as required and click Terminate. An employee can be paid out Annual Leave, TIL/RDO and Long Service Leave is required.

The employee will be marked as terminated on Microkeeper and STP.

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

Payroll Completion

Finalise the Payrun through the recommended 5 step process at the top of the page.

Ensure that payroll data and payment date is correct.

It is recommend that Payslips are backed up by clicking the Backup button.

Back up payrun

An optional step allows select payslips can be loaded by clicking the Print button. This will only display employees payslips who have selected "Employee wants a printed payslip " in their Employee Profile > Employee Display

Print option for Payruns

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

ABA file button on Payrun

Lock the Payrun to make payslips visible to employees. No changes can be made to a Locked Payrun (Unlock the Payrun to make changes)


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


For more information about Single Touch Payroll

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