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Welcome to the Community, Rezk 21!
The bonus pay should be set up like the ordinary time earnings for the employee and will show up as gross earnings of the employee and tag under wage expense account. Then, once you've finalised the pay run, the pay event should be reported and lodged to the ATO.
You'll have to check the payroll journals for the finalized pay run created in QuickBooks Online Payroll and see if there's a GST code BAS - W1 applied to the pay category affected.
To check the payroll journal:
Furthermore, please also check your default payroll chart of accounts under Payroll Settings, and click Chart of Accounts, select Default account if you've set up each categories. You can check these article below to learn more about BAS- W1 and how to match payroll payments in QuickBooks Online:
Feel free to reply to this thread if you need more help with QuickBooks Online. We'll be here to help you. Have a nice day!