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

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

• Step 1. Set up automated super payments with Beam
• Step 2. Configure your pay schedule for super payments
• Step 3. Check super rates are up to date
• Step 4. Process your pay run
• Step 5. 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.
• If you have Beam integration enabled, super payments from pay runs are created as Beam payments by default.
• If you don't have Beam, super payments are created as manual payments by default.
• 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. Set up automated super payments with Beam

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.

You'll need:

• An active QuickBooks Payroll subscription
• Correct business details saved in Payroll Settings

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. 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.
   • 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 3. 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 4. 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 5. 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

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.