Using Deputy Payroll (AU)
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IMPORTANT NOTICE
Information provided by Deputy is intended for general guidance purposes only and is not a substitute for professional legal or financial advice. Deputy does not accept liability for actions taken based on this information. |
Use this guide if your organisation has access to Deputy Payroll Australia. It will help you set up employees for payroll, manage pay runs, submit Single Touch Payroll (STP) information to the Australian Taxation Office (ATO), process superannuation, and access payroll reports.
Tip: Use the topic list below to find the Deputy Payroll (AU) task you’re working on.
In this guide:
- Get started with Deputy Payroll (AU)
- Set up Deputy Payroll (AU) settings and access
- Set up user permissions for payroll
- Set up employee payroll details
- Set up and manage leave with Deputy Payroll (AU)
- Manage recurring payroll items and classifications
- Run a pay run
- Submit STP and complete post-pay run tasks
- Manage superannuation in Payroll AU
- Correct pay and payroll data
- Manage termination pay and employee exit payroll tasks
- View, send, and manage payslips
- View, build, and export payroll reports
- Complete EOFY and STP finalisation tasks
- Fix Payroll AU issues
- Related topics
Get started with Deputy Payroll (AU)
Read these articles to understand Deputy Payroll (AU), complete the initial setup, and check that your business is ready to run payroll.
Before you start
If Deputy Payroll (AU) is not included in your current Deputy plan, you'll need to subscribe first.
Learn about Deputy Payroll AU
Read these articles to understand what Deputy Payroll does and the steps involved in getting your payroll ready.
Prepare for your first pay run
Use these articles to check whether your payroll setup is ready before you process your first pay run.
- Payroll go-live readiness report (AU only)
- How do I switch to Deputy Payroll from another system mid financial year?
Set up Deputy Payroll (AU) settings
Read the articles below to configure business-level payroll settings and control who can access payroll information and workflows.
Manage business-level payroll settings
Read these articles to understand and update your business payroll settings, including business entities and ABN branches.
- Introduction to the Pay tab in Business Settings
- How do I set up multiple business entities in Payroll?
- How do I set up ABN branching in Deputy Payroll?
- How do I add a custom logo for payslips? (Payroll AU)
Set up your organisation's superannuation settings
Read this article to configure your organisation’s superannuation settings and set up a default superannuation fund.
Manage pay calendars
Read these articles to set up pay calendars and assign team members to the correct calendar.
Set up user permissions for payroll
Read these articles to control who can access payroll information and workflows, including sensitive pay rate information.
Set up payroll permissions
- How do I assign user access permissions for Payroll?
- How do I set up the Payroll Manager access level?
Manage sensitive pay rate access
- Managing access to sensitive pay rate information
- Managing access to sensitive pay rate information FAQs
Set up employee payroll details
Before running payroll, check that each employee has the required payroll information in Deputy. Missing or incomplete employee payroll details can affect pay runs, STP submissions, superannuation, and payroll reporting.
Read these articles to add, import, update, and review the payroll information Deputy needs for each employee, including bank, tax, superannuation, pay rate, and employment details.
Add and update employee payroll details
Read these articles when adding payroll details for new employees or updating information for existing employees.
- Onboarding a new team member for payroll using Deputy HR
- Updating an existing team member’s payroll details
- How do I set up and pay salaried employees?
- How do I configure and cost salaried staff in Deputy Payroll (AU)?
Import or bulk update payroll data
Read these articles when you need to add or update payroll information for multiple employees.
- How do I import team member payroll details from another system?
- How do I bulk update team member payroll data (AU only)?
- Payroll go-live readiness report (AU only)
Manage employee superannuation details
Read these articles to set up or update employee superannuation information.
- How do I add or update my team member’s APRA regulated or self-managed superannuation fund details?
- How to add an interim member number for employees joining your default super fund
Manage employee pay and tax details
Read these articles to update pay-related payroll details.
- How are team members’ pay rates updated in Payroll (AU)?
- How do I add extra tax when an employee asks for it?
- How to add multiple bank accounts for employees (Payroll AU and Deputy HR)
Set up and manage leave with Payroll (AU)
Read these articles to understand what changes about leave management when Deputy Payroll AU is enabled, including Payroll AU-managed leave types, leave balances, accruals, leave requests, and Time Off In Lieu (TOIL).
Understand leave management with Payroll AU
Read this article to understand how leave is managed when Deputy Payroll (AU) is enabled.
Set up leave policies, accruals, and balances
Read these articles to set up leave policies and understand how leave accrues and balances are managed.
- Set up leave policies (Deputy Payroll AU)
- Assign leave policies to your team (Deputy Payroll AU)
- Accruing leave (Deputy Payroll AU)
- Leave balances in Deputy and Payroll (Deputy Payroll AU)
Manage leave requests and leave payments
Read these articles to manage leave requests and payments, including NES leave types and parental leave.
- Approve and decline leave requests (Deputy Payroll AU)
- Managers can enter leave requests on behalf of their team members (Deputy Payroll AU)
- Managing National Employment Standards (NES) leave types (Deputy Payroll AU)
- Parental leave (Deputy Payroll AU)
Manage Time Off In Lieu
Read these articles to set up and manage Time Off In Lieu (TOIL), including TOIL pay rate rules.
- Getting started with Time Off In Lieu (TOIL) for Deputy Payroll (AU)
- How to add Time Off In Lieu (TOIL) rules to pay rates (Deputy Payroll AU)
- How to set up a clock-out question for Time Off In Lieu (TOIL) (Deputy Payroll AU)
Manage recurring payroll items and classifications
Read these articles to set up recurring earnings, expenses, deductions, and payroll classifications that affect employee pay and STP reporting.
Set up recurring expenses and deductions
Read these articles to set up recurring employee expenses and deductions, including union fees and child support payments
- How do I set up recurring expenses and deductions?
- How do I add a regular deduction such as union fees?
- How do I set up to withhold child support payments?
Set up recurring extra earnings
Read this article to set up recurring extra earnings, such as allowances and bonuses.
Manage superannuation-related payroll items
Read these articles to set up salary-sacrifice payments and additional employer superannuation contributions.
- How do I add a salary sacrifice superannuation payment?
- How do I create additional employer superannuation contributions?
Understand STP categories and classifications
Read this article to understand the STP categories and classifications used in Deputy Payroll (AU).
Run a pay run
Read these articles to prepare, review, adjust, and process regular or ad hoc pay runs in Deputy Payroll.
Prepare a pay run
Read these articles to prepare a regular pay run or an ad hoc pay run.
Review and adjust a pay run
Read these articles to review employee pay and add or adjust one-off payroll items, including allowances, bonuses, expenses, directors’ fees, and tax.
- How do I review a payslip in a pay run?
- How do I add one-off payroll items to a pay run such as bonuses, deductions and allowances?
- How do I add an allowance?
- How do I add a bonus?
- How do I reimburse expenses?
- How do I pay directors' fees?
- How do I adjust tax on a pay run?
Manage salaried employees
Read this article to set up and pay salaried employees in Deputy Payroll (AU).
Send payslips after the pay run
Read this article to email payslips to multiple team members after you complete a pay run.
Submit STP and complete post-pay run tasks
Read these articles to complete the tasks that happen after a pay run is ready to be submitted or has been locked, including STP and superannuation processing.
Submit payroll information through STP
Read these articles to set up and submit STP information to the ATO, including submissions made by an ATO agent.
- How do I submit the pay run to the ATO via STP?
- When to use an STP Submit or Update event in Deputy Payroll (AU)
- How do I find my software ID to set up STP with the ATO?
- How do I enable ATO Agent STP submissions in Deputy Payroll (AU)?
Process superannuation after a pay run
Read these articles to submit superannuation payments and resolve common SuperStream submission requirements.
- How do I send Superannuation to a superfund clearing house?
- How to avoid duplicate superannuation submissions in Payroll (AU)
- Why must I include gender information for SuperStream payments?
Understand payroll-specific product updates
Read this article to understand the 2025 STSL tax table update in Deputy Payroll (AU).
Correct pay and payroll data
Read these articles when you need to correct payroll information after a pay run, payment, or STP submission.
Correct an incorrect payment
Read these articles to correct an employee’s pay when they have been underpaid, overpaid, or paid incorrectly.
- How do I correct an error in a team member’s pay?
- I underpaid a team member
- I overpaid a team member
Use an ad hoc pay run for a correction
Read this article to prepare an ad hoc pay run when you need to make a payroll correction outside your regular pay cycle.
Correct STP information
Read these articles to submit or update STP information and resolve an STP submission error.
- When to use an STP Submit or Update event in Deputy Payroll (AU)
- Unable to submit STP due to "Length of line should be 120" error
Manage termination pay and employee exit payroll tasks
Read these articles to understand what happens in Deputy Payroll when a team member is terminated and how payroll-linked employee records are handled.
Manage superannuation in Payroll AU
Read these articles to set up and manage superannuation information and payments in Deputy Payroll AU.
Set up business superannuation settings
Read this article to configure your organisation’s superannuation settings and set up a default superannuation fund.
Set up employee superannuation details
Read these articles to add or update an employee’s superannuation fund details, including interim member numbers for your default fund.
- How do I add or update my team member’s APRA regulated or self-managed superannuation fund details?
- How to add an interim member number for employees joining your default super fund
Manage superannuation payroll items
Read these articles to set up additional employer superannuation contributions and salary-sacrifice superannuation payments.
- How do I create additional employer superannuation contributions?
- How do I add a salary sacrifice superannuation payment?
Submit superannuation payments
Read these articles to submit superannuation payments through a clearing house and avoid duplicate submissions.
- How do I send Superannuation to a superfund clearing house?
- How to avoid duplicate superannuation submissions in Payroll (AU)
Understand SuperStream requirements
Read this article to understand why employee gender information is required for SuperStream payments.
View, send, and manage payslips
Read these articles to review, send, download, resend, and access payslips in Deputy Payroll AU.
Review payslips during a pay run
Send payslips to employees
View, download, or resend employee payslips
Help employees access payslips
View, build, and export payroll reports
Read these articles to access payroll reports, build custom reports, check payroll readiness, and export payroll data for accounting or record-keeping.
Check payroll readiness
Read this article to identify payroll setup issues before you go live with Deputy Payroll (AU).
View payroll reports
Read this article to view and export payroll reports for pay runs, employee pay, deductions, superannuation, payroll tax, payslips, and leave entitlements.
Build custom payroll reports
Read this article to create a custom report based on your payroll data.
Export payroll data
Read these articles to export payroll data to your general ledger, including Xero.
- Exporting payroll data to your general ledger in your accounting system
- Exporting payroll data to your general ledger in your Xero accounting system
Complete EOFY and STP finalization tasks
Read these articles to complete end-of-financial-year payroll tasks for Deputy Payroll AU, including STP finalization and related reporting adjustments.
Complete STP finalization
Read these articles to report an EOFY finalization event to the ATO and adjust reportable fringe benefit amounts before finalising STP.
- Reporting an EOFY finalization event to the ATO
- Adjusting Reportable Fringe Benefit Amounts (RFBA) for STP finalization
Review related STP tasks
Read these articles if you need help submitting or updating STP information, setting up your software ID, or enabling ATO agent submissions.
- How do I submit the pay run to the ATO via STP?
- When to use an STP Submit or Update event in Deputy Payroll (AU)
- How do I find my software ID to set up STP with the ATO?
- How do I enable ATO Agent STP submissions in Deputy Payroll (AU)?
Fix Payroll AU issues
Read these articles to troubleshoot common Payroll AU issues, including setup and employee data problems, incorrect pay, STP errors, superannuation issues, and payslip access.
Fix setup and employee payroll data issues
- Payroll go-live readiness report (AU only)
- Why can't I delete team members linked to Deputy Payroll (AU)?
- How do I add or update my team member’s APRA regulated or self-managed superannuation fund details?
Fix pay run and incorrect pay issues
- How do I correct an error in a team member’s pay?
- I underpaid a team member
- I overpaid a team member
- How do I prepare an ad hoc or unscheduled pay run?
- How do I adjust tax on a pay run?
Fix STP submission issues
- How do I submit the pay run to the ATO via STP?
- When to use an STP Submit or Update event in Deputy Payroll (AU)
- How do I find my software ID to set up STP with the ATO?
- How do I enable ATO Agent STP submissions in Deputy Payroll (AU)?
- Unable to submit STP due to "Length of line should be 120" error
Fix superannuation issues
- Why is Beam showing the wrong business address during setup or reconfiguration?
- How is super calculated for employees under 18 in Deputy Payroll (AU)?
- How do I send Superannuation to a superfund clearing house?
- How to avoid duplicate superannuation submissions in Payroll (AU)
- Why must I include gender information for SuperStream payments?
Fix payslip access issues
- How do I review a payslip in a pay run?
- How do I bulk email payslips to my team?
- How do I view, download or resend a team member's payslip from their profile?
- How do I get my payslips from Deputy Payroll (AU)?
Fix leave issues
- Managing Time Off In Lieu (TOIL) for salaried employees without timesheets (Deputy Payroll AU)
- How do I adjust leave balances imported from a previous payroll system?
- How to transfer employee leave balances from a previous payroll system to Deputy Payroll (AU)
Fix Payday Super issues
- Payday Super: What’s changing in Deputy Payroll (AU)
- Payday Super in Deputy Payroll: Start to finish
- Member Verification Requests (MVR) and Deputy’s approach
- How to track super submissions and resolve error messages
- Understanding Qualifying Earnings and Super Liability in Deputy Payroll (AU)
- Sending super contributions via Beam
- Payday Super FAQs
Understand payroll-specific product updates