Set up and manage superannuation in QuickBooks Online Payroll powered by Employment Hero

QuickBooks Payroll now offers HeroClear, Employment Hero’s own real-time super clearing house that pays contributions in real-time, and has built-in fund validation so you can be confident every dollar lands where it should. Beam is still available, and if you’d like to upgrade to HeroClear, getting started is only a click away. 

Use this guide to set up super payments and process pay runs, and stay compliant with the new Payday Super rules starting 1 July 2026. It covers:

• Step 1. (Recommended) Set up HeroClear for automated super payments
• Step 1. (Alternative) Set up Beam for automated super payments
• Step 2. (New) Set up Employee Self Setup (ESS)
• Step 3. Configure your pay schedule for super payments
• Step 4. Check super rates are up to date
• Step 5. Process your pay run
• Step 6. View and report on super payments
• Additional information

Payday Super

From 1 July 2026, super is no longer a quarterly obligation. Under Payday Super, you must pay your employees' super guarantee on payday, at the same time as their salary and wages.

Before you start

• You must be a full admin user to manage super settings.
• You'll need an active QuickBooks Payroll subscription.
• HeroClear is now available and is our recommended clearing house for Payday Super compliance from 1 July 2026. See Step 1 to enable it.
• Beam is still available. If you currently use Beam, you can continue to do so or switch to HeroClear at any time from Payroll Settings.
• If neither HeroClear nor Beam is active, super payments are created as manual payments by default.
• Employee Self Setup (ESS) is now available. It lets new starters input their own payroll details, including super fund choice, directly. See Step 2 to enable it.
• Make sure all employee data in your payroll system is up to date before 1 July 2026. Errors cause delays and ATO issues.

Step 1. (Recommended) Set up HeroClear for automated super payments

QuickBooks Payroll comes with HeroClear built in: a real-time super clearing house that automatically validates fund details and gets contributions where they need to go, fast. It’s the easiest way to meet the 7-business-day deadline under Payday Super.

Why HeroClear?

• Real-time payments via the New Payments Platform (NPP), faster than traditional bank transfers
• Automatic fund validation before payment, so errors are caught before they become penalties
• End-to-end tracking inside QuickBooks Payroll: no file uploads, no portal switching
• Employees can track their contributions in real time via the Employment Hero Work app

Register your business with HeroClear

If you’re an existing Beam user, follow these steps to switch to HeroClear. If you’re a new customer, HeroClear is ready to activate from day one.

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings, then select Superannuation under Business Settings.
3. Select Enable HeroClear. (If you currently use Beam, you’ll see Switch to HeroClear.)
4. Review and accept the HeroClear Terms and Conditions. Select Accept.
5. Confirm your default super fund (see below) and select Save.

Step 1. (Alternative) Set up Beam for automated super payments

Beam is a built-in super fund clearing house. It comes with your QuickBooks Payroll subscription and lets you manage all super tasks from the Employees tab.

Register your business with Beam

Before you start, confirm your business details are correct in QuickBooks. They pre-fill the Beam registration form.

To register:

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings, then select Superannuation under Business Settings.
3. Select Register with Beam.
4. Enter your business details, address, and contact information. Select Next.
5. Enter your payment method and details. Select Next.
6. Choose your default super fund. Select Next.
7. Accept the Terms and Conditions. Select Next.
8. Select Back to payroll.

Your nominated default fund now appears on the Superannuation Settings screen.

Choose a payment method

Beam supports three payment methods for super contributions:

• Direct Debit: enter your BSB, Account Number, and Account Name.
• EFT: select this if you don't want direct debit.
• BPAY: select this if you don't want direct debit.

Any bank account added during setup is automatically available as a refund account for super batch payments.

Set a default super fund

Australian employers must nominate a default fund for employees who haven't chosen one.

• Search for a fund using its USI or ABN, or use Sunsuper Superannuation Fund.
• If you use Sunsuper for a new employee, leave the member number blank. It's automatically generated during the first contribution.

Register multiple employing entities

If your business has more than one employing entity, register each one separately.

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings
3. Select Employing Entities.
4. Select Add and enter the entity details.
5. Select the entity, then select Register with Beam.
6. Follow the standard registration steps above.

Step 2. (New) Set up Employee Self Setup (ESS)

Employee Self Setup (ESS) lets new starters enter their own payroll details, including TFN, bank account, and super fund choice, directly into QuickBooks Payroll via a secure, guided digital form. This means fewer data-entry errors, faster onboarding, and less sensitive information passing through your hands.

Why use ESS?

• Fewer mistakes, less compliance risk: Employees know their own BSB, TFN, and super fund details better than anyone. Direct entry removes transcription errors that cause bounced payments.
• ATO-compliant by default: TFN declarations and super fund choice forms meet ATO requirements, digital and audit-ready, no paper forms.
• Ready to pay from day one: Once a new hire submits, their details flow directly into payroll with no manual entry and no delays to their first pay.
• Works on any device: New hires can complete their self-setup form before they walk in the door.

Enable ESS

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings, then select Employee Self Setup.
3. Toggle on Enable Employee Self Setup.
4. Select Save.

Invite a new employee to complete their setup

1. When adding a new employee, go to Employees and select Add Employee.
2. Enter the employee’s name and email address.
3. Select Send Self Setup Invitation.
4. Your new starter receives a guided digital form to complete their personal details, TFN, bank account, and super fund choice.
5. Once submitted, their details are automatically loaded into payroll, ready for their first pay run.

Step 3. Configure your pay schedule for super payments

Set up your pay schedule so super is created at the right time during every pay run.

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings.
3. Select Pay Schedules.
4. Select an existing pay schedule to edit it.
5. Under Pay run finalisation settings, select the linked word here.
6. In the pop-up, choose when to create a super payment:
   • Immediately: Super payment is created when the pay run is finalised.
     • Recommended for Payday Super compliance.
   • Manually at a later date: You create the super payment from the pay run actions menu.
7. Select Next, then Complete to save.

What happens after finalising:

• If you chose Immediately: Select Review super payment to go straight to the Manage Super Batch Payment screen. Super contributions for that pay run are pre-filled.
• If you chose Manually at a later date: Select Create super payment from the pay run actions menu. You'll be taken to the same Manage Super Batch Payment screen.

Step 4. Check super rates are up to date

QuickBooks automatically updates super rates for pay runs, but only when your settings allow it.

Turn on automatic super rate updates

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings, then Details.
3. Tick Automatically update super rates.
4. Select Save.

This checkbox is ticked by default. If unticked, QuickBooks won't apply any super rate updates.

Check super rates in pay categories

QuickBooks won't auto-update a pay category's rate if the rate is 0%, or if it's different from the applicable rate for the current financial year.

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Go to Payroll Settings, then Pay Categories.
3. Select each pay category and check the Super Rate field.
4. Update any rates that don't match the current financial year rate.

To audit all pay categories at once:

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Go to Payroll Settings, then Pay Categories.
3. Select Export, choose your file type, and select Download.
4. Open the file and review the Default Super Rate column.
5. Update any rates in QuickBooks, then save.

Check pay rate templates

Review any custom pay rate templates your business has created (not Award-linked templates).

QuickBooks won't update the super rate in a template if:

• The Override checkbox is ticked, or
• The rate is 0% or different from the current financial year rate.

To find and audit templates:

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Go to Payroll Settings, then Pay Conditions, then Pay Rate Templates.
3. Select Export, choose your template and file format, then Download.
4. Open the file and review the Super Rate columns.
5. Update any values, save the file, then re-import it into QuickBooks.

Check super rates in employee pay rates

For employees not linked to a pay rate template, check their individual pay rates.

QuickBooks won't update a rate automatically if:

• The Override checkbox is ticked, or
• The rate is 0% or different from the current financial year rate.

Review the Super Rate fields in each employee's Pay Rates section and update as needed.

Step 5. Process your pay run

To process a pay run:

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select New Pay Run.
3. Select any applicable settings then select Create.
4. Update the pay run as needed, then select Finalise Pay Run.

When you finalise a pay run, super contributions are created based on your pay schedule settings from Step 2.

Check super payment status

After finalising a pay run, you can track your super's status on the Pay Runs page. Hover over the super icon next to the Date Paid column.

Step 6. View and report on super payments

Track the status of previous payments or generate filtered reports for your records.

View previous super payments

1. Go to Reports and select Standard reports (Take me there).
2. Select Super Payments (located under Payroll).
3. Select the ID number to view additional information for a super payment.

Run a super contribution report

1. Go to Reports and select Standard reports (Take me there). 
2. Select Super Contributions (located under Payroll).
3. Apply the relevant filters then select Run Report.

Create a super payment batch

1. Go to Reports and select Standard reports (Take me there)..
2. Select Super Payments (listed under Payroll).
3. Select New Super Payment Batch.
4. Select the appropriate filters (for example, Date Range, Pay Schedule, Contribution type) and then select Filter.
5. Select Create Batch.
6. Select Submit.
7. Select your Payment Method
   • If you select Direct Debit you’ll be prompted to select a Bank Account and Refund Bank Account (where undelivered super amounts are returned to).
   • If you select EFT or BPAY, tick the acknowledgement checkbox to review thePayment Details which will appear on the screen along with payment instructions. These instructions will also be emailed to the payroll admin.
   • Make sure that the reference number and amount of the super payment are correct when paying the super batch.

Additional information

HeroClear vs Beam: which should I use?

Switching from Beam to HeroClear

You can switch at any time from Payroll Settings > Superannuation. Your historical Beam payment data is preserved. Upgrading to HeroClear is only a click away.

Opt out of automatic super rate updates (optional)

If you don't want QuickBooks to update super rates automatically, you can turn this off.

1. Go to All apps , select Payroll, then select Employees (Take me there).
2. Select Payroll Settings.
3. Under Business Settings, select Details.
4. Untick Automatically update super rates.
5. Select Save.

Warning: If you opt out, you must update super rates manually every financial year. Missing a rate update can cause non-compliance.