STP Quick Setup

This guide is tailored for small businesses with 1 to 10 employees.

If your business fits this category and you want a straightforward way to prepare for reporting to the Australian Taxation Office (ATO) using Single Touch Payroll (STP), follow the following three steps.

Step 1: Entering Employee Details

Start by entering accurate details for yourself and your employees.

  1. Go to Menu > Settings > Employees.
  2. Click Edit next to the employee you're adding information for.
  3. Scroll down to the "Payment and Employment" section.

Depending on your employees' pay structure, choose one of these options:

  1. Consistent Hours and Hourly Pay
  2. Fixed Salary Payments
  3. Variable Lump Sum Payments

For consistent hours and hourly pay

Payment and Employment Example

For fixed salary payments

Payment and Employment Example

For variable lump sum payments

Payment and Employment Example

If you're unsure of the Hourly Rate, use the Salary calculator. Enter the Basic Hours, select how often you pay your employee, then enter the Yearly Salary into the empty field. The Rate field will update based on that Salary. 

Complete the Payment and Employment section, then update other relevant details like TFN and Super.

The page will auto-save as you make changes.

Step 2: Creating and Reviewing Payrun

  1. Go to Menu > Payroll > Payrun.
  2. Click New Payrun to start.

    Example of a generating a Payrun
    Payrun example

  3. Most details should be correct if your Global Settings are accurate.
  4. Select the appropriate payrun if it's your first one.

  5. If it's the first payrun of the financial year, ensure the expected number of payruns is accurate. Microkeeper will predict how many payruns are likely based on your payment date in arrears value.

  6. Click Payrun when details are correct.

  7. The earned amount from Employee Profile will appear. Click Payslip to review the payslips for the payrun.

    Example of a generated Payrun
    Payrun example

  8. Below is a Payslip example. You can edit any of the payslip items using the provided buttons.

    • Click the Add button  to add a Payslip Item to any area of the Payslip.
    • Click the Edit button to edit any values or details of the Payslip.
    • Hover your mouse left of the edit button to Delete a Payslip item.

    Employee Payslip

  9. Once you ensure Payslips are accurate, click the Lock button at the top of the page.


Step 3 - STP Lodgement and Submission 

Before submitting, inform the ATO that Microkeeper is your Standard Business Reporting software:

  1. Add Microkeeper Software ID to ATO's Access Manager. The ID can be found on the upper left in the Global Settings page.

  2. Notify ATO through their Access Manager or by phone. Once notified, proceed to lodge the report.

  3. Go to Payroll > Payruns > Payslip > STP Lodge after locking a Payslip.


  4. On the STP Lodge page choose "Normal Payrun" (see the next section for EOFY process) and select "Submit" as event type then click Review Data.

  5. Correct any errors, click I have reviewed data, tick box to sign ATO Agreement, and click Lodge STP.


End of Financial Year Process 

At the end of the financial year, submit a "Final" STP Lodgement to the ATO:

  1. Create a Payrun as usual.
  2. After locking, click STP Lodge.
  3. Select "Final Payrun" instead of "Normal Payrun".

    STP Lodge Final
  4. Lodge as normal and check your income statement on your MyGov Portal.

If your system pre-Microkeeper didn't lodge STP 

If you started using Microkeeper mid-year without prior STP submissions, you will need to enter the earnings for the start of the year into Microkeeper before you can process your final run.

  1. Enter year-start earnings in Payroll > Payruns > New Payrun.
  2. When selecting the period, make sure you're selecting a period from before you started in Microkeeper. 
  3. Click Payrun. You will likely see an empty payslip, or the normal one generated.
  4. You will need to amend this run to reflect the total figures paid in the financial year before starting with Microkeeper. Click Payslip to open that run.
  5. Edit/add payments for accuracy.

    If there is already a before tax payment on the payslip you can amend it by clicking the small grey edit button on the right-hand side of the payment.
    Then change the Rate to match the amount paid in the beginning of the financial year. If there isn't you will need to add the before tax payment using the blue Add button.

    Payslip Payments

  6. Ensure tax figure represents total PAYG tax paid before Microkeeper use. To edit this, click the grey Edit button and change the value.
    Payslip Deductions

  7. Once you have entered all the pre-Microkeeper figures into the Payslip, continue to submit the final STP lodgement for the financial year.