This is part of our Payroll, Super and STP Phase 2 series (Chapter 5 of the MYOB tutorial hub):

• Lesson 1: Setting Up Payroll in MYOB
• Lesson 2: Adding Employees in MYOB with STP Phase 2 Categories
• Lesson 3: Setting Up Superannuation and Pay Super in MYOB
• Lesson 4: Moving to STP Phase 2 in MYOB
• Lesson 5: Running a Pay Run and Reporting STP in MYOB
• Lesson 6: Running a Test Pay Cycle in MYOB Before Going Live
• Lesson 7: End of Year Payroll Finalisation in MYOB

STP Phase 1 was switched off on 27 February 2025, meaning every employer now needs to be reporting under Phase 2.

1. What is actually different in Phase 2

Rather than one gross pay figure, Phase 2 requires pay broken into categories like ordinary hours, overtime, allowances and bonuses separately.

2. Checking your current setup is compliant

If your file was set up before this change, it is worth confirming your pay items and leave categories are correctly mapped to Phase 2 categories.

3. Employment basis and income type

Phase 2 also requires an income type and employment basis for each employee, which affects how their data is reported.

4. Getting a second opinion if unsure

Given how easy it is to miss a mapping detail, having someone familiar with STP Phase 2 review your setup is worthwhile.

5. Common mapping mistakes to check for

Most STP Phase 2 issues in MYOB come down to a handful of repeat problems, worth checking even if you believe your file is already compliant:

• Allowances lumped into ordinary pay instead of being coded to their own allowance category.
• Leave categories left unmapped after being added, so paid leave doesn’t report correctly.
• Employment basis set incorrectly (e.g. casual staff marked as part-time), which affects how the ATO reads your data.
• Termination payments not itemised into their correct ETP or unused leave categories.

None of these stop a pay run from processing, which is exactly why they tend to sit unnoticed until an ATO discrepancy notice or an EOFY finalisation flags them.

6. Getting a second opinion if unsure

Given how easy it is to miss a mapping detail, having someone familiar with STP Phase 2 review your setup is worthwhile.

7. FAQ: STP Phase 2 in MYOB

What is STP Phase 2?
An expansion of Single Touch Payroll reporting that breaks pay down into detailed categories (ordinary hours, overtime, allowances, leave and more) instead of one gross figure, giving the ATO and Services Australia more detailed, real-time payroll data.

Do I still need to do anything about STP Phase 2 in MYOB?
Yes, if your file was set up before the change. STP Phase 1 was switched off on 27 February 2025, so every employer now needs to be reporting under Phase 2 – it’s worth confirming your pay items, leave categories and employee details are still mapped correctly.

What happens if my MYOB file isn’t STP Phase 2 compliant?
Pay runs will usually still process and report, but the underlying data reaching the ATO can be inaccurate, which tends to surface later as a discrepancy at EOFY finalisation rather than an immediate error.

MYOB Academy has STP Phase 2 transition guidance: academy.myob.com. Our registered BAS agents can review your payroll mapping for compliance.