Processing Bonus and Commission Payments

Overview

This article explains how to process bonus and commission payments in a pay run using Myaccountant. It includes steps to create a new pay item (if needed), enter the payment amount, and optionally override tax or super.

Step-by-Step Instructions

  1. Open the Pay Run and Employee Record
  1. Go to Payroll > Pay Runs.
  2. Open the relevant pay run.
  3. Click on the employee’s name to open their pay record.
  1. Add the Bonus or Commission Pay Item

If the Pay Item Already Exists:

  1. Click Add Pay Item.
  2. Select Bonus or Commission from the list.
  3. Click Add.

If You Need to Create a New Pay Item:

  1. Click Add Pay Item, then click New Pay Item (top-left).
  2. Fill in the following:
    • Name : e.g. "Performance Bonus" or "Sales Commission"
    • Payment Type: Select Bonuses and Commission from the dropdown.
  3. Click Save.
  4. Then select the new pay item and click Add to include it in the employee’s pay run.

The pay item name must be unique — duplicate names will trigger an error.

  1. Enter the Bonus or Commission Amount
  1. Click the pencil icon in the Actions column for the pay item.
  2. In Qty/Hours, enter 1.
  3. In Rate, enter the full amount of the bonus or commission.
  4. Click Save.

If you're paying based on units or percentages, adjust Qty/Hours and Rate accordingly.

  1. (Optional) Override Tax and Super Amounts

If you need to manually change the auto- calculated tax or super:

  1. Click the Edit Tax and Super button.
  2. To override:
    • Tax : Enter your custom tax amount in the tex field.
    • Super: Enter your custom super amount in the Super field ( if different) 
  3. Click Update to apply changes.

Use overrides only if you're confident about the correct tax/super amounts—these override the ATO-calculated values.

  1. Review Final Output
  • The bonus or commission payment will appear on the employee’s payslip.
  • It will also be reported correctly via STP under the "Bonus and Commission" category.

Tips:

  • Use specific names for recurring bonuses or commissions (e.g. “Quarterly Sales Bonus”) for easy tracking.
  • If unsure about the correct tax treatment, consult your accountant or the ATO's guidance on lump sum payments.
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