A guide to Single Touch Payroll Phase 2 (STP2) Compliance check

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If you've been treating Single Touch Payroll Phase 2 (STP2) as a "set it up once and forget it" job, payday super just changed that.

What's actually changed

Since 1 July 2026, employers have had to pay superannuation guarantee (SG) contributions within 7 business days of each payday, rather than quarterly. To enforce this, the ATO now requires STP2 submissions to include two additional data points: Qualifying Earnings and Super Liability. In plain terms, the ATO is using your STP2 categorisation to calculate what you should have paid, and comparing it against what you did pay, on every single payday.

Why a "sloppy" STP2 setup is now a bigger deal

Before payday super, an under-configured STP2 category - an allowance mapped incorrectly, an OTE definition left incomplete - was mostly a reporting inconsistency. Now, because the ATO derives your super liability directly from those categories, the same misconfiguration can make it look like you underpaid super, even if the payment itself went out on time and in full. The compliance risk has moved upstream, from "did you pay on time" to "was your setup accurate in the first place."

The good news: there's a grace window

The ATO has published a risk-based compliance approach (PCG 2026/1) for the first year of payday super, running 1 July 2026 to 30 June 2027. Employers who make genuine efforts to pay on time and correct errors as soon as they're identified sit in the ATO's "low-risk zone." Translation: catching and fixing your own setup issues now is exactly the behaviour the ATO is rewarding.

Take 5 minutes to check your setup

Open your STP2 settings and confirm every pay item - wages, allowances, bonuses - is mapped to the correct category.
Run a test pay run and check the super liability figure matches what you'd expect.
Check for and resolve any open ATO "action required" flags on your account.

That's it. It won't catch every possible issue, but it clears the most common ones - and it's a good habit to build into your processes in the new financial year.

If you want fewer things to check manually

QuickBooks Payroll Advanced tracks STP2 categorisation and super liability in real time and flags drift before it turns into an ATO compliance issue - worth a look once you've run your own check.