Payroll

Process employee payments, manage pay categories, and handle compliance.

Overview

The Payroll module handles:

• Pay run processing
• Pay categories (earnings, deductions, allowances)
• Award interpretation
• Tax calculations (PAYG)
• Superannuation
• Payslip generation
• STP (Single Touch Payroll) reporting

Employee Pay Settings

Before processing payroll, ensure employees have pay settings configured. These live on each person's record in People Management:

Setting Up Pay Details

1. Go to employee profile

1. Configure:

• Pay schedule (Weekly, Fortnightly, Monthly)
• Pay rate (Hourly, Salary)
• Base rate amount
• Tax scale
• Super fund details

Tax File Declaration

1. Employee completes TFD form

• Tax file number
• Residency status
• Tax-free threshold claim
• HELP/HECS debt
• Other withholding variations

Pay Categories

Types of Pay Categories

Earnings

• Ordinary hours
• Overtime
• Penalty rates
• Allowances
• Bonuses
• Commissions

Deductions

• Tax (PAYG withholding)
• Superannuation
• Salary sacrifice
• Union fees
• Health insurance

Allowances

• Travel allowance
• Tool allowance
• Uniform allowance
• Meal allowance

Creating Pay Categories

1. Configure:

• Name and code
• Type (Earning, Deduction, etc.)
• Calculation method
• Tax treatment
• STP category mapping

Awards and Agreements

Award Configuration

1. Add or select an award
2. Configure:

• Base rates
• Penalty rates
• Overtime multipliers
• Leave loading
• Allowances

Rate Interpretation

The system automatically:

• Applies correct rates based on day/time
• Calculates penalties for weekends/public holidays
• Handles overtime thresholds
• Manages casual loading

Award Library

Mployr maintains a library of Australian Modern Awards so you don't have to build rates from scratch:

1. Browse or search the award library by code or name
2. Open an award to see its classifications, rates, penalties, allowances, and overtime rules
3. Apply an award to the relevant employees so their pay is interpreted automatically

Reviewing Award Updates

Awards change - through annual wage reviews and variations. When an award you use is updated, Mployr flags it so you can review and apply the changes:

1. Open the award (a review prompt appears when an update is available)

1. Confirm the changes so the new rates flow into future pay runs

This keeps you compliant without manually re-keying rates each time an award moves.

Flexible Arrangements

Beyond standard pay, Mployr supports common flexible pay and leave arrangements under Payroll > Arrangements:

Time Off In Lieu (TOIL)

Record overtime taken as time off rather than paid out:

1. Set how time accrues and how it's taken
2. Track the employee's TOIL balance

Individual Flexibility Arrangements (IFA)

Capture an agreed variation to award or agreement terms for an individual:

1. Record the terms that have been varied and the agreed dates
2. Keep it on file as your record of the arrangement

Annualised Arrangements

Set up an annualised salary that covers award entitlements:

1. Configure the salary and the entitlements it absorbs
2. Use it to support reconciliation against award rates

Processing a Pay Run

Step 1: Create Pay Run

1. Select:

• Pay schedule
• Pay period dates
• Payment date

Step 2: Add Employees

1. Select employees for this pay run

Step 3: Review Payslips

For each employee, review:

• Hours and earnings
• Deductions
• Super contributions
• Net pay

Step 4: Make Adjustments

Add one-off items:

• Bonus payments
• Expense reimbursements
• Leave payouts
• Additional deductions

Step 5: Calculate

1. System calculates:

• Gross pay
• Tax withholding
• Super guarantee
• Net pay

Step 6: Approve and Finalize

1. Review pay run summary
2. Submit for approval (if required)
3. Manager approves

Step 7: Process Payments

1. Generate ABA file for bank
2. Upload to your bank
3. Mark as paid

Final and Redundancy Pay Runs

When an employee is terminated, create a final pay run to pay them out correctly:

1. The termination type affects tax treatment (for example, genuine redundancy is taxed differently) - check the figures before finalising
2. Finalise and pay as you would a normal pay run, and report via STP

Payslips

Viewing Payslips

Employees access payslips via:

1. Navigate to profile

1. Select pay period
2. View or download PDF

Payslip Contents

• Pay period dates
• Gross earnings breakdown
• Deductions breakdown
• Super contributions
• Net pay
• YTD totals
• Leave balances

Distributing Payslips

Options for distribution:

• Email to employees
• Available in self-service portal
• Print for manual distribution

Superannuation

Super Guarantee

• Automatic calculation at 11.5% (2024-25)
• Applied to ordinary time earnings
• Tracked per employee

Reporting Super

1. Review contributions by fund
2. Generate clearing house file
3. Submit payments

Super Funds

Manage employee super:

• Default fund setup
• Employee choice of fund
• Multiple funds per employee

Tax and Compliance

PAYG Withholding

• Automatic tax calculation
• Uses ATO tax tables
• Handles all scale types
• Adjusts for HELP/HECS

Single Touch Payroll (STP)

1. Pay run is finalised
2. System generates STP file
3. Submit to ATO
4. Track submission status

Payment Summaries

• Generated annually
• Available in employee portal
• Submitted via STP Phase 2

Reports

Payroll Reports

• Pay run summary
• Earnings by category
• Deductions summary
• Super contributions
• PAYG summary
• Leave liability

Exporting

• CSV/Excel exports

• Bank payment files
• Compliance reports

Troubleshooting

An employee's hours didn't appear in the pay run

The pay run loads approved timesheets only. If hours are missing, check that the employee's timesheet was approved in Time & Attendance before you added them to the pay run, then recalculate.

An employee's pay calculated as zero or looks wrong

Most often the employee's pay settings aren't complete. Open their profile, check the Pay Settings and Tax Declaration tabs (pay rate, pay schedule, tax scale), then return to the pay run and click Calculate Pay Run again.

The rates in a pay run look out of date

Awards change through annual wage reviews and variations. Open the award under Payroll > Awards - if an update is available a review prompt appears. Use Review & Update to step through the changes and confirm them so the new rates flow into future pay runs.

I can't finalise the pay run

Finalising is the last step after review. Work through the steps in order - Calculate Pay Run, then submit for approval if your business requires it and have the manager approve - before Finalize Pay Run becomes available.

Redundancy is being taxed like normal pay

Redundancy belongs on a final pay run, not a standard one. Terminate the employee from their profile first (see the People Management guide), then create a final pay run - the termination type drives the tax treatment, so genuine redundancy is taxed correctly. Check the figures before finalising.

Frequently asked questions

How is superannuation calculated?

Super guarantee is calculated automatically at 11.5% (2024-25) on ordinary time earnings and tracked per employee. Review contributions by fund and generate a clearing house file under Pay > Super.

How do I report pay to the ATO?

When a pay run is finalised, Mployr generates a Single Touch Payroll (STP) file. Submit it to the ATO and track the submission status from the pay run. Keep the confirmation on file.

How do I pay an employee who's leaving?

Create a final pay run for them. Mployr includes outstanding entitlements - unused leave, any owed amounts, and redundancy where applicable. See the People Management guide for terminating the employee first.

Can I record overtime as time off instead of paying it out?

Yes - set up a TOIL (Time Off In Lieu) arrangement under Payroll > Arrangements, configure how time accrues and is taken, and track the employee's TOIL balance.

How do I pay employees from the finalised pay run?

After finalising, generate the ABA file under Process Payments, upload it to your bank, then mark the pay run as paid.

Tips

• Process pay runs on a consistent schedule
• Review and approve timesheets before pay run
• Check super contributions quarterly
• Keep tax declarations current
• Reconcile payroll to general ledger monthly
• Store STP submission confirmations