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Payroll 9 min read

How to Run Payroll in XIntelliSync (Australian STP Phase 2)

"Payroll isn't hard. Payroll compliance is. Here's how the OS handles both."

Payroll in Australia isn't just "pay people." It's PAYG withholding, super guarantee at 12%, leave accrual, STP Phase 2 reporting, and Fair Work Act compliance — across a single pay run. XIntelliSync handles the calculation. You handle the review.

Running a Pay Run

Step-by-step process for each pay period:

  • Step 1: Navigate to Payroll → Pay Runs → Create Pay Run
  • Step 2: Select pay period (weekly, fortnightly, or monthly)
  • Step 3: Review employee hours, leave, and any adjustments
  • Step 4: System calculates gross pay, PAYG withholding, super (12%), and net pay
  • Step 5: Review the pay run summary — check every line
  • Step 6: Approve and process — STP report generates automatically
  • Step 7: Download ABA file for bank payment

After the Pay Run

Once processed:

  • STP Phase 2 report is ready for lodgement via the ATO Business Portal
  • Pay slips are generated for each employee
  • Super liability is tracked against quarterly deadlines
  • Leave balances update automatically
  • Payroll expense entries flow into your P&L

XIntelliSync prepares your STP report. You review and lodge via the ATO Business Portal. XIntelliSync does not lodge directly with the ATO.

Common Questions

Does XIntelliSync handle STP Phase 2?

Yes. Pay runs generate STP Phase 2 compliant reports with disaggregated gross, income types, and country codes as required by the ATO since January 2024.

How is super calculated?

Superannuation Guarantee at 12% (2025-26 rate) is calculated automatically on ordinary time earnings for all eligible employees. The system tracks accumulation against quarterly deadlines.

Can I generate ABA files for bank payment?

Yes. After processing a pay run, XIntelliSync generates an ABA payment file that you upload to your bank for direct deposit. XIntelliSync prepares the file — your bank processes the payment.

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