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

Go to employee profile

Click Pay Settings tab

Configure:

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

Casual employees no longer carry an assumed 38-hour week. Where a casual has no set hours, Mployr shows their average actual hours instead of a notional full-time figure, so estimates and leave projections reflect what they really work.

Tax File Declaration

Employee completes TFD form

Enter details in Tax Declaration tab:

Tax file number
Residency status
Tax-free threshold claim
HELP/HECS debt
Medicare levy exemption or reduction
Withholding variation and any extra withholding

The tax declaration now drives PAYG withholding directly: a Medicare exemption selects the correct tax scale (Scale 5 or 6), a family reduction is applied, and any withholding variation or extra withholding amount is honoured. If you change an employee's declaration while a pay run is still open, Mployr recalculates that pay run so the change takes effect immediately rather than next period.

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

Navigate to Pay > Pay Categories

Click Add Category

Configure:

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

Awards and Agreements

Award Configuration

Go to Pay > Awards

Add or select an award
Configure:

Base rates
Penalty rates
Overtime multipliers
Leave loading
Allowances

Rate Interpretation

The system automatically:

Applies correct rates based on day/time - penalty bands apply to the hours that fall inside each window, not to the whole shift
Calculates penalties for weekends and public holidays
Handles overtime thresholds, including daily overtime where the award sets an explicit daily cap
Manages casual loading

Charges meal-break penalties where an award requires a payment when a break isn't given, including public-holiday and multiply-current-rate variants

Reckons day boundaries in the business's payroll timezone, so hours at the start and end of a period aren't lost

Clamps the ordinary base of a standard adult employee up to the National Minimum Wage in force for the pay period ($26.44/hr, $1,004.90/wk from 1 July 2026) as a safety net, and notes it as a compliance warning. Juniors, apprentices and trainees are lawfully paid a percentage of the adult rate, so they are never floored to the adult minimum

Employees who aren't covered by an award are paid the National Minimum Wage plus casual loading where applicable - award penalties are not applied to them.

Public holidays are paid only for days the employee ordinarily works, and King's Birthday is treated as state-specific rather than national. Salaried, full-time and part-time employees can be marked as having worked a public holiday without needing a timesheet.

If someone edits a timesheet after a pay run has been calculated, the pay run automatically reverts to draft so the change can't be missed.

Award Library

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

Go to Payroll > Awards

Browse or search the award library by code or name
Open an award to see its classifications, rates, penalties, allowances, and overtime rules
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:

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

Use Review & Update to step through what's changed

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:

Go to Payroll > Arrangements and create a TOIL arrangement

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

Individual Flexibility Arrangements (IFA)

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

Create an IFA arrangement

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

Banked TOIL is paid out automatically on termination as part of the final pay run.

Annualised Arrangements

Set up an annualised salary that covers award entitlements:

Create an Annualised arrangement

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

Rostered Days Off (RDO)

Where an award builds RDOs by accruing hours over a cycle:

The award's own rules drive how RDO hours bank up
The banked balance is visible against the employee
Taking an RDO pays the day off from those banked hours rather than as extra pay

Simply viewing an RDO balance no longer creates one - balances appear once hours actually accrue.

Processing a Pay Run

Step 1: Create Pay Run

Navigate to Pay > Pay Runs

Click New Pay Run

Select:

Pay schedule
Pay period dates
Payment date

Step 2: Add Employees

Click Add Employees

Select employees for this pay run

System loads approved timesheets from Time & Attendance

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

Click Calculate Pay Run

System calculates:

Gross pay
Tax withholding
Super guarantee
Net pay

Step 6: Approve and Finalise

Review pay run summary

Clear the STP Phase 2 pre-flight - Mployr checks the pay run for anything that would be rejected on lodgement, such as an incomplete tax file declaration, and flags it before you submit rather than after

Submit for approval (if required)
Manager approves

Click Finalise Pay Run

A pay run is blocked from finalising while there are unresolved problems that would produce wrong pay - an award-covered employee who has been flat-rated, an open missed clock-out, or an employee with no super destination. Resolve the flagged item and recalculate.

Step 7: Process Payments

Generate ABA file for bank
Upload to your bank
Mark as paid

Final and Redundancy Pay Runs

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

Terminate the employee from their profile (see the People Management guide)

Create a final pay run for that employee

Mployr includes their outstanding entitlements - unused leave, any owed amounts, and, where applicable, redundancy amounts

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

Payslips

Viewing Payslips

Employees access payslips via:

Navigate to profile

Click Payslips tab

Select pay period
View or download PDF

Payslip Contents

Pay period dates
Gross earnings breakdown
Deductions breakdown
Super contributions, each with its Payday Super due date
Net pay
YTD totals
Leave balances, plus what was taken this period

A daily breakdown attributing each day's pay to the day it was earned, with clock times shown in the business's payroll timezone

Distributing Payslips

Options for distribution:

Email payslips straight from the finalised pay run, either to everyone or to selected employees. You can override the recipient, subject and message, and if an employee has no primary work address Mployr falls back to any email on file

Download all payslips for a pay run in one go

A secure view link so an employee can open their payslip in a browser without logging in

Available in the self-service portal
Print for manual distribution

Where a send fails, the pay run reports the actual reason for that employee rather than a blanket success.

Superannuation

Super is calculated automatically at the Super Guarantee rate for the financial year - 12% for 2026-27 - on ordinary time earnings, and tracked per employee with a Payday Super due date against each contribution.

For stapled fund lookups, the annual maximum contribution base, choice-of-fund handling and the full super workflow, see the Superannuation guide.

Tax and Compliance

PAYG Withholding

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

Single Touch Payroll (STP)

STP lodgement is not switched on yet. Mployr builds the complete Phase 2

payload and records the lodgement against the pay run, but **nothing is

transmitted to the ATO. A submission made now is stamped Simulated** and

carries a SIM- reference so it can never be mistaken for a real one. Keep

lodging through your existing channel until this is enabled. SuperStream is

the same: contributions are calculated and recorded, and are not transmitted.

Pay run passes the STP Phase 2 pre-flight check
Pay run is finalised
Mployr generates the STP file with the full Phase 2 payload

Submit - the lodgement is recorded against the pay run and marked Simulated

Track the submission status on the pay run

The pre-flight flags STP Phase 2 readiness per employee before lodgement - an incomplete tax file declaration is the most common blocker.

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

General ledger journals (for Accounting)

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 Finalise 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 the rate for the financial year - 12% for 2026-27 - on ordinary time earnings, capped against the annual maximum contribution base, and tracked per employee. See the Superannuation guide for the detail.

Why won't the pay run finalise?

Mployr blocks finalisation while something would produce wrong pay or a rejected lodgement. The usual causes are an award-covered employee who has been paid a flat rate, an employee with an unresolved missed clock-out, an employee with no super destination, or an incomplete tax file declaration failing the STP Phase 2 pre-flight. Fix the flagged item, recalculate, then finalise.

I changed a timesheet and the pay run went back to draft

That's deliberate. Editing a timesheet behind a calculated pay run reverts it to draft so the new hours are picked up - recalculate and the change flows through.

How do I email payslips?

From the finalised pay run, use the email option to send to everyone or to selected employees. You can override the recipient, subject and message, and download all payslips at once. Each employee can also be given a secure link to view their payslip without signing in.

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

In this guide