Payroll | Help Centre

Payroll

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

Overview

The Payroll module handles:

Pay run processing
Pay categories (earnings, allowances, deductions and more)
Award interpretation
Tax calculations (PAYG)
Superannuation
Payslip generation
STP Phase 2 readiness checks - STP itself is lodged through Xero
Payroll compliance checks and records
Sending pay runs to Xero

You'll find it under People > Payroll in the sidebar: Pay Runs, Awards, Arrangements, Compliance and Settings.

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 the Remuneration tab

Click Set Up Pay (or edit the Current Pay Settings)

Configure:

Effective From - the date the settings start to apply
Award and classification
Employment type (Full Time, Part Time or Casual - Contractor, Labour Hire and Voluntary are also listed)

Pay basis (Salary or Hourly - casuals are always hourly) and pay schedule (Weekly, Fortnightly, Monthly, Quarterly), or a Pay Cycle Preset, which sets the schedule for you

Base salary or hourly rate, and hours per week and per day

Super Rate (%) - it matches the Super Guarantee rate unless you untick Match super guarantee rate (12%)

Annual leave loading - As per award, None, or a Specified rate

No modern award covers this employee (award-free) - tick it for someone no award covers, so they aren't flagged as missing an award

The tax scale comes from the employee's tax file declaration on the Tax tab, and their super fund is recorded on the Super tab.

Pay settings are dated. Work from the Effective From date is paid on the new settings - including the days after it in a pay period it falls part-way through - while earlier periods keep the settings that were in force then, even when they're recalculated. A future date takes effect on that day, and Pay History shows each version as current, scheduled, or replaced before it took effect.

A salaried employee who starts or leaves part-way through a pay period is paid for the days they were employed, not the whole period.

An employee with no award gets no annual leave loading unless you choose Specified rate (for example 17.5% under their contract or a policy).

Casual employees have no set hours. Their Remuneration tab shows Average Hours / Week (last 12 wks) from their timesheets (No timesheet history yet until there is some), and they're paid for the hours they actually work.

Tax File Declaration

Employee completes a tax file number declaration - employee onboarding doesn't collect it (its tax step just says the employer will ask for it separately), so the employer records it

Open their Tax tab and click Lodge a tax file declaration (or Update Declaration), then record:

Tax File Number - the employee's answer to question 1 of the declaration (see below)

Residency Status - Australian Resident, Foreign Resident, Working Holiday Maker or Seasonal Worker

Whether they claim the tax-free threshold
HELP and other study and training loan debts
Medicare levy exemption (full or half) or reduction
Withholding variation and any extra withholding, plus any tax offset

Save the declaration

Mployr doesn't hold tax file numbers yet - that needs ATO approval - so there's no box for the number itself: keep it wherever you hold it now. Under Tax File Number, choose what the employee answered, and the hint under the box says how it's withheld:

TFN quoted - normal rates. The declaration shows the TFN as quoted and held outside Mployr

Applied for a TFN - normal rates for 28 days from the Declaration Date, then the no-TFN rate until a TFN is quoted

Exemption: under 18, earns below the tax-free threshold or Exemption: receives a pension, benefit or allowance - normal rates

Not quoted - every pay is withheld at the no-TFN rate, 47% (45% for a foreign resident)

A new declaration can't be saved until this is answered, and updating a declaration keeps the answer already saved - an older declaration saved with a TFN Pending exemption asks for the answer again. Everything else on the declaration is used for pay as normal.

The tax declaration drives PAYG withholding directly: a Medicare exemption selects the correct tax scale (Scale 5 or 6) for a resident claiming the tax-free threshold, a family reduction is applied, and any withholding variation or extra withholding amount is honoured. If you change a withholding detail on 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 - a run awaiting approval or approved moves back to draft and needs approving again. Finalised pay runs aren't changed.

Pay Categories

Types of Pay Categories

Mployr sets up a standard set of pay categories for your business. Each has a category type:

Earnings

Ordinary hours
Overtime
Penalty rates and shift loadings
Casual loading
Bonuses
Commissions

Allowances

Travel allowance
Meal allowance
Car allowance
Laundry allowance
Tool allowance

Deductions

Union fees
Workplace giving
Salary sacrifice (super)

Other types

Superannuation - Super Guarantee and employer additional super

Leave - annual, personal/carer's, long service and compassionate leave

Reimbursement - expense reimbursements

PAYG tax withheld is worked out for you.

Creating Pay Categories

Open Pay Categories - it isn't in the main menu, so owners and admins add it as a shortcut with Customise Quick Launch in the sidebar

Click Add Category

Configure:

Code and Name

Category Type (Earnings, Deductions, Allowances, Superannuation, Leave or Reimbursement)

STP Category

Rate Type, Default Rate and Multiplier

Whether it's Taxable and whether super applies (Super Applicable)

Click Create Category

Awards and Agreements

Award Configuration

Most businesses use an award from the library (see Award Library below). To build an award of your own:

Go to People > Payroll > Awards

Click Add Award - Quick Select can fill in the code and name of a common award - enter the Award Code, Effective Date and Award Name, and click Create Award

Build its rates on the award's tabs:

Classifications

Pay Conditions

Rules - penalty and overtime rules

Rate Labels

Pay Rates - base and penalty rates

Allowances

Leave

Shift Settings

Settings - casual and annual leave loading

Library awards can't be edited directly - Adopt one to get a copy your business can change.

The last tab, Changes, lists who changed the award's rows, newest first - what was added, changed or removed, with each field's old and new value, plus adoptions and accepted or skipped updates.

Award Settings for Your Business

Some awards have options that apply only to your business - such as harvest, vintage or crushing seasons, piecework, rostered days off, averaged hours, sleepovers, broken shifts or site allowances. To set them, go to People > Payroll > Awards and, in the Awards that apply to this business card, click Settings beside the award (it only appears for awards that have options like these). The dialog lists only the options that award uses, and changes affect your business only. An option marked Not automatic is recorded as your policy but isn't applied to pay automatically. Click Save settings to finish.

For an award with seasonal rules, switch on Apply seasonal rules and click Add season for each season - give it a name if you like, its Starts and Ends dates, and whether it repeats Every year (optionally until a Repeat until date) or Does not repeat. You can add as many seasons as you need. Where the award defines a standard season, Use the award's standard season adds it and Mployr works out its dates each year.

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
Counts paid leave and public holidays towards the weekly ordinary-hours limit, so hours worked beyond it in a week that includes leave are paid as overtime
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
Keeps a salary whole when part of it moves to another line - a public holiday or an RDO taken - so the lines always add back to exactly the salary for the period
Never pays an employee aged 21 or over (going by the date of birth on their record) an ordinary rate below the National Minimum Wage for the pay period - $26.44 an hour ($1,004.90 a week) from 1 July 2026. Employees under 21 are paid junior rates and aren't raised to the adult minimum

Hourly employees who aren't covered by an award are paid their own rate or the National Minimum Wage, whichever is higher (plus casual loading for casuals), with no weekend, public holiday or overtime penalty rates. Salaried employees without an award are paid their salary.

Public holidays are paid only for days the employee ordinarily works - judged from their last six weeks of timesheets, so a new starter, or salaried staff without timesheets, are paid the holiday - 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: the calendar button on their row in the pay run opens Public Holidays Worked, and Works public holidays on their pay settings sets the starting point.

If someone edits a timesheet after a pay run has been calculated, the pay run recalculates - a run awaiting approval or approved moves back to draft first - so the change can't be missed. A timesheet in a finalised pay run can't be edited.

Award Library

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

Go to People > Payroll > Awards

Browse the list, or search by award name, code or industry

Open an award to see its classifications, rates, penalties, allowances, and overtime rules. Adopt, in a library award's row menu, makes a copy your business can customise

Mark the award Applies to us - from the row's actions, in bulk, or on the award itself. Award interpretation only runs for awards that apply to your business, and an award with employees on it that hasn't been switched on is flagged Not activated

Apply the award to the relevant employees - their award and classification are set on their pay settings - so their pay is interpreted automatically

Reviewing Award Updates

Awards change - through annual wage reviews and variations. Library awards are kept up to date by Mployr. If you've adopted a copy of an award, Mployr flags it when the library award it came from has a newer version, so you can review and apply the changes:

Open your copy of the award (an Update Available banner appears when there's a new version)

Click Review Update to step through what's changed

Tick the changes you want and click Accept Selected so the new rates flow into future pay runs - or Skip This Update

Lines your business changed itself are shown as kept, and accepting an update doesn't write over them.

Pay runs use the award rates in force on the first day of the pay period, so a period that started before an increase is paid at the old rates.

Flexible Arrangements

Beyond standard pay, Mployr supports common flexible pay and leave arrangements under People > Payroll > Arrangements, which has TOIL, IFA and Annualised Wage tabs, and on the Arrangements tab of an employee's record. Employees see their own arrangements on the Arrangements tab of My Profile.

Time Off In Lieu (TOIL)

Record an agreement to take overtime as time off rather than have it paid out:

Go to People > Payroll > Arrangements, open the TOIL tab and click New TOIL (New TOIL agreement while the tab is empty)

Choose the employee and award, and record the Overtime hours worked, when it was worked, the Agreement date and the Consume window (months). In OT hourly rate ($) enter the employee's ordinary hourly rate, and pick the OT multiplier - payouts are the rate times the multiplier

Click Create TOIL Agreement

Both the employer and the employee sign it - open the agreement from the TOIL row on the employee's Arrangements tab and add the signers under Signatures. The award requires a separate written agreement for each amount of overtime

Track how much is still owing on the agreement

Once both have signed, the overtime the agreement banks is held back from the pay run for the period it was worked, so it isn't paid twice. Until both have signed, it isn't an agreement: the overtime is paid in that pay run as normal, and the pay run notes that the hours are also in the bank.

Mployr doesn't have a screen for recording TOIL taken as time off yet - the hours Still owing only go down when they're paid out. Use Request payment on the agreement to have the hours still owing paid out instead, in the pay period after the request. Unused TOIL is paid out automatically on the employee's next pay run once its window expires, and banked TOIL is paid out on termination as part of the final pay run, as overtime. Each payout is paid once - if the pay run or payslip that paid it is deleted before it's finalised, the hours go back to the agreement.

Individual Flexibility Arrangements (IFA)

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

On the IFA tab, click New IFA and choose the employee, the award and the clauses being varied

Click Test against the award - the better off overall test prices the terms against the award minimum over the employee's worked time in the 13 weeks before the agreement date (creating the IFA runs the test if you haven't)

Write the BOOT statement, record the agreement and start dates, and save
Collect the signatures on the arrangement's page, and keep it on file as your record of the arrangement

Terms that leave the employee worse off can't be made. Someone with the authority - a business owner or admin by default - can overrule a failed test after a clear warning, and their name, authority and reason are recorded permanently against the arrangement. An IFA can't be made before the employee has started, and their start date must be on record.

Annualised Arrangements

Set up an annualised salary that covers award entitlements:

On the Annualised Wage tab, click New Arrangement (New arrangement while the tab is empty)

Configure the salary and the award clauses it satisfies
Use it to support reconciliation against award rates

Pay runs only apply an annualised arrangement once it's signed - by the employer, and by the employee where the award requires their written agreement. Where the employee's onboarding includes the award arrangements step, they read and sign it there. Recording the employer's signature isn't available on screen yet, so until it is, the employee is paid under the award as normal. Once it applies, the arrangement is reconciled against the award on the hours the employee actually worked, and any shortfall a reconciliation finds is paid as a back payment on the next pay run. When the employee leaves, the final pay run reconciles the arrangement and pays any shortfall.

Rostered Days Off (RDO)

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

Switch the scheme on: under People > Payroll > Awards, click Settings beside the award in Awards that apply to this business and turn on Run an RDO scheme

The award's own rules drive how RDO hours bank up - banks accrue when a pay run is finalised, and a day of paid leave or a public holiday counts towards the RDO where the award treats it as a day worked

The banked balance is visible against the employee on the Leave tab of their record, and for everyone banking hours under People > Time > Rostered Days Off (shown only where your award has RDOs)

Taking an RDO pays the day off from those banked hours rather than as extra pay. On Rostered Days Off, use the buttons on the employee's row to record a rostered day off (Record RDO) or adjust the RDO bank (Record adjustment, with a reason) - or Record a day off and Adjust on their Leave tab

Balances appear once hours actually accrue - an employee shows on Rostered Days Off once a pay run has been finalised for them on an RDO scheme. Banked RDOs still owing when someone leaves are paid out on the final pay run as part of the employment termination payment, with no super.

Processing a Pay Run

Step 1: Create Pay Run

Navigate to People > Payroll > Pay Runs

Click New Pay Run

Under Pay Period Details, select:

Pay cycle preset, or the pay period type
Pay period dates
Payment date

Run Type - Ordinary pays the period from its timesheets, leave and salary. Back pay and Adjustment pay only the lines you add - arrears, a missed allowance, a bonus or a correction for a period already paid

Click Next

Cycles that already have a pay run are labelled in the Pay Cycle list - you can still pick one for a back pay or adjustment run. Each day is paid by one ordinary run: an ordinary run refuses anyone already paid for those days by another ordinary run that hasn't been voided.

Your business needs a location with its state recorded under Business > Locations before payroll will run - public holidays and long service leave are set by state law, so without one a pay run can't be created, calculated or finalised.

Step 2: Add Employees

Under Select Employees, choose who's in this pay run and click Next

Check the details under Review & Create, then click Create Pay Run

System loads the period's hours from timesheets in Time & Attendance

While the run is a draft you can bring in more people with Add Employees. An employee on a different pay schedule from the run is refused - pay them on a run for their own schedule, or change their pay schedule first.

Step 3: Review Payslips

For each employee, review:

Hours (including paid leave) and earnings
Deductions
Super contributions
Net pay

Banners on the pay run flag timesheets or leave requests for the period still awaiting approval, and unresolved missed clock-outs, each with a Review link.

Step 4: Make Adjustments

While the pay run is a draft, open a payslip with View Payslip and use Add Line for one-off items (once the run is submitted for approval, its payslips can't be changed):

Bonus payments
Expense reimbursements
Leave payouts
Additional deductions

Choose the Line Type and a Pay Category of that type, then enter the Quantity/Hours and Rate - the line's amount is the quantity times the rate times the pay category's multiplier. For a one-off amount such as a bonus, enter a quantity of 1 and the amount as the rate, on a category whose multiplier is 1. The line is taxed, and counted for super, as its pay category says. For a Lump Sum E category (back pay earned more than 12 months ago), choose the Financial year it belongs to - it's reported to the ATO against that year.

Step 5: Calculate

A pay run is calculated as soon as it's created. Click Calculate again after you change anything that feeds it - timesheets, leave, pay settings or a tax declaration. It works out:

Gross pay
Tax withholding
Super guarantee
Net pay

Mployr records what each payslip was calculated from. If an employee's time, leave or RDOs change after that - a shift clocked off after you clicked Calculate, say - Finalise is refused, naming who and what changed, and the run goes back to draft to be recalculated, submitted and approved again.

Step 6: Approve and Finalise

Review pay run summary

Click Submit for Approval

An approver clicks Approve

Click Finalise

A pay run is blocked from finalising while there are unresolved problems that would produce wrong pay:

The business has no state on record
An employee already paid for a day of the period by another finalised pay run
An open or auto-closed missed clock-out in the period
Two of an employee's time entries that overlap, so the same hours would be paid twice
Time, leave or RDOs that changed after the run was calculated (the run goes back to draft)
A rejected timesheet in the period - or, where your business requires approval before hours are paid, any timesheet still in draft or awaiting approval
An employee with super owing and no super destination
An award-covered employee who has been flat-rated
A part-time employee whose award pays overtime past the hours agreed each day, with no part-time agreement and no hours per day on their pay settings

Where you've switched on Stop a pay run that pays award staff without their award (People > Payroll > Settings, General Preferences), an employee with no award and classification who isn't marked award-free

An employee on a different pay schedule from the run
Where your books are kept in Mployr, a payment date that falls in a closed or locked accounting period

Resolve the flagged item and recalculate.

The pay run also checks STP Phase 2 readiness - anything that would be rejected on lodgement, such as an incomplete tax file declaration - and lists it per employee with a Fix link.

Step 7: Process Payments

Click Download ABA on the finalised pay run and choose the account you're paying from (or enter its BSB and account number). Anyone with missing or invalid bank details is listed first - fix them, or download anyway for the rest

Upload the file to your bank

If your pay runs go to Xero, pay them from Xero instead - see Payroll through Xero. Xero lodges the figures it holds, so Download ABA and Email All Payslips aren't offered on a pay run that goes to Xero unless its Xero panel says Sent, when Mployr and Xero hold the same figures.

Where your business has its chart of accounts in Mployr's Accounting module, finalising also posts the pay run's journal to the general ledger, dated the payment date.

How Leave Is Paid

Approved leave in the pay period is paid from the leave request itself - it isn't entered on a timesheet - and it's paid from the employee's balance, only up to that balance:

Leave that accrues a balance - such as annual leave, personal/carer's leave and long service leave - is paid up to what the employee has available for that leave type when the pay run is calculated, taken in date order across the year's leave. Hours beyond that are unpaid (leave without pay) - for a salaried employee they come off the period's salary
Leave granted per occasion, such as compassionate leave, and family and domestic violence leave are paid in full

Where a request has Pay the remainder as Annual Leave switched on, hours its own balance can't cover are paid from the annual leave balance instead, with annual leave loading; anything annual leave can't cover is unpaid

Public holidays inside annual or personal/carer's leave are paid as public holidays and don't use the balance

Negative Caps on the employee's Leave tab let a balance go below zero by up to the hours you set, and pay honours them

When the pay run is finalised, the paid hours move from Pending to Taken on the employee's balance, any unpaid hours are released, and the period's leave accrual is added - so this period's accrual counts towards later periods, not this one

Leave only accrues in Mployr from your first pay run here, so an employee whose balance hasn't been brought in has nothing to draw on and their leave is paid as unpaid. Carry in opening balances before you pay leave, under People > Time > Leave > Leave settings - see Time & Attendance.

Sending a Pay Run to Xero

If you lodge payroll through Xero, a finalised pay run can be sent there. What to do each pay run once it's set up is in Payroll through Xero.

Under Business > Integrations, open the Xero connection with Configure. In Sync Configuration, switch on the Pay Runs export (and Leave Applications, so leave reaches Xero) and click Save Settings - exports start switched off

Under Payroll Reference Data, click Import Payroll, then use Change beside each Xero earnings rate, deduction type, reimbursement type and leave type to pick the matching pay category or leave type. Super funds are matched by USI or ABN

In Sending Pay Runs to Xero, check Pay calendars - where Xero has more than one calendar of a frequency, or you pay two pay cycles of one frequency, choose the calendar for each row (Mployr refuses the send rather than guess). Under PAYG withholding, choose Xero calculates it (the default) or Mployr's figure is lodged, and set First pay run to send if earlier runs were paid by your previous system

Pair each employee with their Xero employee under Employee Mapping - they must be on the matching Xero pay calendar

A finalised pay run is sent automatically while the export is on. The Xero panel on the pay run shows Sent or Not sent - click Send to Xero to send it now, or Send again after you fix something

What to expect:

The run arrives in Xero as a draft on the matching pay calendar. Posting it and filing it with the ATO are still done in Xero

If Xero already has a draft for the same period on that calendar, Mployr fills it in. A draft for a different period blocks the send until it's posted or deleted in Xero, because Xero allows only one draft per pay frequency. If the calendar is next due for a different period, nothing is created - add the pay run in Xero (Payroll > Pay runs > Add pay run) and send again, and Mployr fills in that draft

An earnings or allowance line whose pay category isn't linked to a Xero earnings rate is refused - that employee's payslip isn't written. It's never guessed as ordinary hours, which would have Xero accrue super on it and report it under the wrong STP category. The pay run tells you how many warnings the send raised; the details, including the category code to link, are in Sync History on the Xero connection

Leave goes to Xero as a leave application, not a payslip line

Mployr's super guarantee is the one sent: where Xero works out a different figure, Mployr's amount replaces it. With Xero calculates it, a PAYG figure in Xero that differs from Mployr's stops the send at Needs review, listing the difference per employee

A run mixing staff of two pay cycles that go to different Xero calendars is refused - pay each cycle in its own pay run
Final pay runs can't be sent to Xero - record the termination pay in Xero directly
Voiding a run after it was sent leaves its draft in Xero - delete it there

Pay the run and send its payslips from Xero, which lodges it. Download ABA, Email All Payslips and Submit STP aren't offered on a pay run that goes to Xero - the first two come back if its Xero panel says Sent

Pay runs, timesheets and leave aren't imported back from Xero while Mployr sends them there, because Xero's copy would be written over Mployr's

Pay runs paid before the First pay run to send date on the Xero connection aren't sent to Xero, and are paid and reported as before

Final and Redundancy Pay Runs

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

Terminate the employee (see the People Management guide)

Once their termination date has passed, find them on the Employees list - add Terminated to the status filter - open their actions and choose Create Final Pay Run

Mployr includes their outstanding entitlements - unused annual leave (with loading) and long service leave, banked RDOs, TOIL and any annualised wage shortfall. Enter any redundancy amount (shown for redundancy termination types, with the NES minimum for guidance) and any Payment in Lieu of Notice. The Termination Preview shows the figures before you create the run, including banked RDOs (paid inside the employment termination payment, with no super) and any TOIL paid out as overtime

Unused leave and banked RDOs are priced at the employee's own rate, never below their award's ordinary rate for their classification on their last day
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

A final pay run can't cover days a finalised pay run already paid the employee for - start it the day after their last paid day - and is refused while the employee is still in another open pay run, which it names.

Payroll Settings

People > Payroll > Settings holds the business-wide payroll options:

Pay Cycle Presets - the pay schedules used when you create pay runs and timesheets

Employment Defaults - values applied when onboarding new employees

Default Super Fund - where super goes when an employee hasn't chosen a fund (see the Superannuation guide)

Payslip Leave Balances - whether payslips show leave balances, and which leave types

Payslip Daily Breakdown - whether payslips include a per-day breakdown

Royal Queensland Show - shown only for a business in Queensland: Observe the Royal Queensland Show makes the Ekka a public holiday for pay, rosters and leave. It's set from your addresses to start with, and you can change it

Unpaid Breaks - break rules for employees whose award has no break clause (off by default; an award always wins)

Clock-In Window & Paid Time - how early staff can clock on, and whether time outside a rostered shift is paid

General Preferences - the financial year and other global settings, including Warn on missing timesheets and Stop a pay run that pays award staff without their award (off by default)

Payslips

Viewing Payslips

There's no payslip list on an employee's profile - each payslip reaches the employee as a secure link that opens it in a browser without logging in, with Download PDF:

When a pay run is finalised, each employee with an Mployr login gets a Your payslip is ready notification with View Payslip

When you email payslips from the pay run (see below), each employee gets the link by email

From the pay run, use View Payslip to open any employee's payslip and Download PDF.

Payslip Contents

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

Leave balances, plus what was accrued and taken this period, on the PDF when Show leave balances on payslips is on (it is by default). Long service leave can be held back until the employee is entitled to take it with Only show long service leave once the employee is entitled (Payroll Settings > Payslip Leave Balances)

A daily breakdown of hours and earnings by the day they were earned, when Show daily breakdown on payslips is switched on in Payroll Settings > Payslip Daily Breakdown. On the pay run's own copy of the payslip, payroll staff always have a Daily Breakdown with clock times in the business's payroll timezone

Distributing Payslips

Options for distribution:

Email All Payslips - each employee is emailed a secure link to view and download their payslip - nothing is attached. Anyone without an email address is listed first, so you can fix it or Send anyway to the rest. The button appears once the pay run is approved, but the links only open once it's finalised, so send after finalising

Email payslip from a single payslip (once the pay run is finalised), where you can override the recipient, subject and message. 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 ZIP of PDFs

Print for manual distribution

When a single Email payslip fails, Mployr shows the reason. Email All Payslips sends in the background, so check with anyone who says their payslip didn't arrive.

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 - 7 business days after the pay run's payment date, or 20 business days for an employee's first contribution to a new fund (see the ATO's Payday Super guidance at ato.gov.au).

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 is lodged through Xero. Mployr doesn't send pay runs to the ATO, so a pay run has no Submit STP. SuperStream is the same: contributions are calculated and recorded in Mployr, and are not transmitted.

To lodge a pay run:

Finalise the pay run in Mployr
Post it in Xero - posting a pay run in Xero lodges it with the ATO

If your pay runs go to Xero, Mployr sends each finalised run there as a draft for you to post - see Payroll through Xero.

The pay run still checks STP Phase 2 readiness and lists anything missing with a Fix link. An incomplete tax file declaration is the most common thing it flags.

Payment Summaries

Under STP, employees get their income statement through myGov rather than a payment summary from you
Income statements come from what Xero lodges

Payroll Compliance

People > Payroll > Compliance gathers the obligations that sit beside the pay run:

Superannuation timing - contributions from finalised pay runs that are past their due date and haven't been recorded as received by the fund, with the amount and days late per employee. Once your clearing house confirms payment, click Record received on the employee's row (or Record all as received), enter the Date the fund received it - the day the fund received the money, not the day you sent it - and an optional Payment reference, then click Record as received. That takes it off the list. Super the fund received after its due date was paid late, and attracts the super guarantee charge, which is lodged with the ATO separately

Fair Work statements - employees never given the Fair Work Information Statement, and casuals still owed the Casual Employment Information Statement

Casual conversion - casual conversion notices whose response is overdue

Employee records - employee records must be kept for seven years and produced on request. Download Pay records, Hours, Superannuation, Leave and Employment basis as CSV files

Reports

Payroll Reports

Templates in the Reports module's gallery - Pay Run Summary, Payslips - Current Period, Super Contributions YTD, Tax Withheld YTD, Pending Leave Requests and Leave Taken by Type (YTD)

Your own reports built on the Payroll data source, one row per payslip - gross earnings, tax withheld, super, allowances, deductions, net pay, YTD totals, and hours worked, with ordinary, overtime and leave time in minutes

Records downloads by category on People > Payroll > Compliance

Exporting

Excel, CSV or PDF exports of the reports you build

Bank payment files (Download ABA) - a pay run that goes to Xero is paid from Xero

Payslip PDFs (Download All Payslips)

Compliance records (People > Payroll > Compliance)

General ledger journals aren't exported - they're posted to Accounting automatically when a pay run is finalised.

Troubleshooting

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

The pay run loads the hours on each employee's timesheet for the period - approval isn't what brings them in. If hours are missing, check the employee is in the pay run and that their entries are on a timesheet for the right dates in Time & Attendance, then click Calculate again. A shift that's still clocked in, or was auto-closed after a missed clock-out, isn't paid until it's confirmed or corrected - the pay run lists these with a Review link. Hours can't be recorded for days before the employee started or after they left.

An employee's leave was paid as unpaid

Leave is paid only up to the employee's balance for that leave type when the pay run is calculated - see How Leave Is Paid. Check their Leave tab: if their balance from before Mployr was never brought in, carry in the opening balance under People > Time > Leave > Leave settings (or adjust the balance on the Leave tab), then click Calculate again while the pay run is still a draft.

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 Remuneration and Tax tabs (pay rate, pay schedule, award and classification, and tax declaration), then return to the pay run and click Calculate again. Also check:

Their award is marked Applies to us under People > Payroll > Awards - award interpretation doesn't run for an award that hasn't been switched on, and the Awards page warns Award interpretation is off for the people affected, with an Activate button

They have a classification as well as an award
An hourly or casual employee has timesheet hours for the period - without them only leave is paid

The tax looks right - a declaration answered Not quoted, or Applied for a TFN more than 28 days ago, withholds at the no-TFN rate

The rates in a pay run look out of date

Pay runs use the award rates in force on the first day of the pay period, so a period that started before an increase is paid at the old rates. If you use an adopted copy of an award, open it under People > Payroll > Awards - an Update Available banner means the library award has a newer version. Use Review Update to step through the changes and accept 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, Submit for Approval, and have an approver Approve - before Finalise becomes available. If it still won't finalise, the message names the blocker (see Step 6).

Redundancy is being taxed like normal pay

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

Xero refused some payslips

An earnings or allowance line whose pay category isn't linked to a Xero earnings rate is refused rather than guessed. Find the category code in Sync History on the Xero connection, then under Payroll Reference Data click Change beside the right Xero earnings rate and pick that pay category (click Import Payroll first if it isn't listed). Then click Send again on the pay run - or Send to Xero if nothing reached Xero.

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. The usual causes are an award-covered employee who has been paid a flat rate, an unresolved missed clock-out, overlapping time entries, time or leave that changed after the run was calculated, a rejected (or, where approval is required, unapproved) timesheet, an employee with no super destination, an employee on a different pay schedule, or a business with no state on record. Fix the flagged item, recalculate, then finalise. STP Phase 2 issues such as an incomplete tax file declaration don't stop finalising, but should be fixed before the pay run is lodged.

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

That's deliberate. Editing a timesheet behind a pay run that's awaiting approval or approved moves the run back to draft and recalculates it, so the new hours are picked up - submit it for approval again. A timesheet in a finalised pay run can't be edited.

How do I email payslips?

Finalise the pay run, then click Email All Payslips - each employee is emailed a secure link to view and download their payslip (links sent before the run is finalised don't open until it is). To send just one, or to override its recipient, subject and message, open the payslip and use Email payslip. Download All Payslips downloads them all at once.

Where do I find my payslips? (employees)

Open the link Mployr sends you: when a pay run is finalised you get a Your payslip is ready notification, and your employer may also email you the link. It opens your payslip in a browser, with Download PDF. There's no payslip list on My Profile - if you can't find a payslip, ask your payroll contact to email it again.

How do I submit Single Touch Payroll (STP)?

Through Xero. Mployr doesn't send pay runs to the ATO: finalise the pay run in Mployr, then post it in Xero, which lodges it. If your pay runs go to Xero, Mployr sends each finalised run there as a draft for you to post.

How do I pay an employee who's leaving?

Create a final pay run for them from the Employees list once their termination date has passed. Mployr includes outstanding entitlements - unused leave, banked RDOs and TOIL - and you enter any redundancy or payment in lieu of notice. See the People Management guide for terminating the employee first.

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

You can make a TOIL agreement under People > Payroll > Arrangements for the overtime worked, signed by the employer and the employee - once both have signed, that overtime is held back from the pay run. Mployr can't record the time off being taken yet, though - the hours stay owing until they're paid out, which happens automatically when the agreement's window expires or employment ends, or sooner with Request payment.

How do I pay employees from the finalised pay run?

After finalising, click Download ABA, choose the account you're paying from (or enter its BSB and account number), and upload the file to your bank.

Tips

Process pay runs on a consistent schedule
Review and approve timesheets before pay run
Carry in opening leave balances before your first pay run with leave in it

Check super contributions against their due dates after each pay run, now that Payday Super applies, and record them as received on People > Payroll > Compliance

Keep tax declarations current
Reconcile payroll to general ledger monthly
Keep the STP confirmations from Xero

In this guide