Payday Super FAQs

New ATO Payday Super rules take effect from 1 July 2026.

These rules require all Australian employers to pay super at the same time as wages, with contributions required to reach employees' funds within 7 business days.

To support this, the new Payday Super Assist integration can automatically handle your super payments through the SuperChoice clearing house each time you submit a pay run.

For more information, or to enable the Payday Super Assist integration in your HR system, please contact your account manager.

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Setting Up Payday Assist

How do I set up the Payday Assist integration?

Instructions about how to enable the Payday Super integration and set up your SuperChoice account will be provided once it has been approved for your account.

Once the SuperChoice integration is approved, you will need to:

• Update to HR version 5.4.8 or later
• Verify all employee and super fund information is complete and correct in HR
• Register and set up your account with SuperChoice
  • Go to www.employerpay.com.au/EmployerPortal/register/custodian/megabus and follow the provided Employer Self Enrolment user guide

• After registering with SuperChoice:
  • Enable Payday Super Assist integration in HR
    (following the provided Payday Super Assist Set Up guide)
  • Warning: If the integration is enabled before registering with SuperChoice, your pay runs will send files to SuperChoice which will be rejected

Changing to SuperChoice

How do I change to the SuperChoice clearing house?

If you decide to use the Payday Super Assist integration, you will need to go to www.employerpay.com.au/EmployerPortal/register/custodian/megabus and follow the provided Employer Self Enrolment user guide to enrol your business.

When to Change Clearing Houses

When should I change clearing houses?

If you are using the Payday Super Assist integration, you should switch over to SuperChoice immediately.

You must also set up the Payday Super integration with SuperChoice before commencing the first pay run for the new financial year, so that the super payment file can be automatically submitted.

When to Enable Payday Assist

Do we enable the Payday Assist integration in HR before or after final pay run of the financial year?

It is up to you whether you want to start using SuperChoice and the Payday Assist integration.

You can continue to use your old clearing house/method to process payments prior to June 30 (see below).

However, if you are using Payday Super Assist, it must be enabled for the first pay run of the new financial year.

First Pay Run

Do we need to set up the SuperChoice pay period as 01/07/26 or as our next pay run day?

Employers must comply with the PayDaySuper rules from the first pay run being paid on or after July 1 2026.

However, you can complete the set up instructions we have provided earlier than this and commence using the SuperChoice integration earlier if you wish.

Mandatory Usage

Is the use of Payday Super Assist integration mandatory, or can I use another clearing house/method?

It is not mandatory to use the Payday Super Assist integration.

You are welcome to use alternative clearing houses or methods to meet the ATO's payday super requirements.

However, the Payday Super Integration provides an easy and automatic method for continually meeting these requirements as an HR user.

Manual Usage

I manually enter super payment details into our SuperChoice portal, can I still do it this way or will it be mandatory to use the exported file?

You can still enter your SuperStream information in the SuperChoice portal manually, if desired—just do not enable the integration in HR.

You should also sign up using the generic SuperChoice registration portal, rather than the provided Megabus link.

SuperChoice Registration

Not all questions that appear on the onboarding guide are being asked when registering with Super Choice (eg. number of staff)?

The provided onboarding document is a generic guide supplied by SuperChoice.

Just follow the process and enter all of the the information as required when registering through the Megabus portal and ignore any missing steps or fields from the guide.

ABNs

Do I enter my own company's ABN or Megabus's in the SuperChoice portal?

You should enter your own company's ABN.

Direct Debit vs Credit

What is the difference between Direct Debit or Direct Credit?

Direct Debit: SuperChoice pulls the payment from your nominated bank account when the payment is made—you authorise the debit and they initiate it.

Direct Credit: You push the funds to SuperChoice in advance—you initiate a transfer to their account before the payment run, so the money is already sitting with them when they process contributions.

• Warning: If the funds aren't already with SuperChoice when the SuperStream file is submitted, when using Direct Credit, then the payment will fail.

If you initially set up as direct credit are you able to change it to direct debit?

Yes, you can change between Direct Debit and Direct Credit at any time using the Superchoice portal.

Registration Completion

What happens when I complete my SuperChoice registration?

You will receive an email to the address you signed up with confirming your registration.

To start using the Payday Super integration, you then need to enable it in HR, as per the provided instructions.

Returning to the Portal

Once set up, is there any need to return to the SuperChoice portal again, or is it all done in HR?

There is no need to return to the SuperChoice portal once the integration is set up, unless there are errors with your submissions.

If there are no errors, the payments should be handled completely automatically whenever a pay run is processed in HR.

Can't Log In

I can't log into the SuperChoice portal after i have registered does not work?

It is likely that you are trying to log in to the general SuperChoice website instead of the Megabus/SuperChoice portal at: http://www.employerpay.com.au/megabus

If you cannot log in at the link above:

• You may have self-registered on the general SuperChoice website instead of using the Megabus link in the set up instructions
• In this case, please re-register using the link above.

We recommend bookmarking the Megabus SuperChoice Portal link in your browser for easy access.

Employee Details

Do I need to manually enter my employees' super fund details into the SuperChoice portal?

No, the Payday Assist integration automatically enters the data in the SuperChoice portal when you finalise a pay run.

However, if a new employee with the generic Funded Super fund is included on a pay run, you will need to enter their details and pay their super manually, using the SuperChoice portal.

Switching Clearing Houses

How do I switch to SuperChoice from another clearing house?

Switching to the Payday Super integration with SuperChoice will replace your previous clearing house:

• The previous clearing house registration will no longer be used
• Employee super contributions will continue to be paid into the same funds

If there were costs associated with the previous clearing house:

• Contact the provider and advise them of the change

Not Using SuperChoice

What if I don't want to use SuperChoice as my clearing house?

If you decide not to use the Payday Super Assist integration, then nothing will change for you.

You will still need to generate the SuperStream file and manually upload it to your clearing house of choice.

Uploading to Other Clearing Houses

How do I upload my super payment files to other clearing houses?

See the SuperStream help guide for further information about generating and uploading SuperStream files.

Confirming Submissions

How do I know if my SuperStream submission has been received by SuperChoice?

To confirm your SuperStream submission has been received:

• Log in to your SuperChoice portal at http://www.employerpay.com.au/megabus
• Click on the Contributions tab at the top
• You should see your contribution in the list below
  • If there are no issues, it will have a green tick next to it
  • If a red issues icon next to it, see Submission Validation Issues below

Submission Validation Issues

What if there are issues with my submissions to SuperChoice?

Once the email functioality has been enabled by SuperChoice, you will receive a confirmation email for each submission sent to them from your Marlin HR system.

If the Status shown indicates issues (e.g. Member Matching Exceptions), you need to correct the issues in the SuperChoice portal before it will be processed.

The SuperChoice portal displays any issues requiring your attention with red icons and highlights the missing or incorrect information in a different colour.

Where appropriate, it will also provide you with appropriate selections. to resolve the issues.

It is important that you:

• Address these issues immediately, so that the submission can proceed and payment can reach the employee funds within the 7 day deadline
• Update the information in Marlin HR, so that future submissions can be processed without your intervention

See the guide below for further help handling SperChoice rejections.

If you need further assistance in using the SuperChoice portal, please search for help inside the portal or reach out to
SuperChoice support.

Super Fund Rejections

A super fund may reject a payment made to them by SuperChoice (e.g. due to an incorrect employee Fund Member Number or an incorrect Fund selected on the employee in Marlin HR) and credit the payment to your account.

In this case, you need to correct the information in HR to ensure submissions from future pay runs are accepted and manually re-process the rejected payment using the SuperChoice portal.

You need to login to the SuperChoice portal, insert/correct the relevant data and click on Submit for the processing of the submission to continue.

You also need to insert/correct the information in HR so that the next submissions process through SuperChoice without issue.

Fund Employer Number (FEN) Errors

How do I correct a Fund Employer Number (FEN) validation error?

The Fund Generated Employer ID field in HR should normally be blank.

Never enter anything into this field, unless a super fund writes to you with a unique identifier code and asks you to include it in all communications with them—in our experience, this is very rare.

If you inadvertently enter something into this field, your super payment submissions will not pass validation in the SuperChoice portal, until you perform the following steps.

In the SuperChoice Portal:

• Navigate to Employer Maintenance
• Open the Employer record
• Click on the Manage Funds tab
• Employer has the option to Manage FENs:
  • Either Edit the FEN to correct it (pencil icon)
    
  • Or, Remove the FEN entirely if it has been mistakenly included (rubbish bin icon)
    

After completing the correction:

• Return to the Contributions listing
• Click on the Re-Validate icon (circled in yellow below)

Make sure to also remove the Fund Generated Employer ID in HR to avoid further issues.

Payment Frequencies

How long does it take for super payments to be made from SuperChoice, once my file has been automatically uploaded?

Payment times will vary, depending on the receiving super funds.

However, payments should usually only take between 24–48 hours to be made, once the SuperStream file has been received.

Advance Payments

What happens when I pay staff in advance?

Pay runs automatically generate and send the super payment files to ensure employers don't miss payment deadlines.

If you process a pay run in advance the super payments will be processed though SuperChoice immediately, regardless of when you pay the wages from bank.

Payment Confirmations

How do I know if my super payments have been made, once the file has been uploaded?

We are currently working with SuperChoice to provide confirmation emails, once the super payments have been made.

In the meantime, you can check the status of your payments by logging into the portal.

Employees Without Super Funds

What if I don't have super fund details for an employee?

Employees cannot be included in the SuperChoice payment file without complete fund details.

If fund details are not yet available:

• Remove the employee from the current pay run by unticking them
  • This allows other employees to be paid
• Once their fund details have been entered in Employee Maintenance:
  • Run a separate pay run for that employee for the same period
  • This will generate a SuperChoice submission for that employee's super payment

If the pay run cannot be delayed:

• Assign a generic fund that is not ticked for inclusion in the SuperStream payment file (e.g. Funded Super)
  • This allows the employee to be paid and their super to be calculated
• You will then need to manually pay their super via the SuperChoice portal for each affected pay run until correct fund details have been entered

482 Visas

How do I process employees on 482 Visas?

Employees on a 482 visa are set up the same as other employees.

To configure super for a 482 visa employee:

• Open their Employee Maintenance record in Edit mode
• Click on the Entitlements tab
  • Tick the Apply Compulsory Rate checkbox
  • Enter any Additional Rates, if required
  • Add their Super Fund and Member Number

Earnings and allowance types must be configured as Qualifying Earnings (formerly OTE):

• Any hours or payments entered against these types will be included in the super calculation.
• They will also be included in the SuperStream submission sent to SuperChoice, for payment into the employee's selected fund.

ATO SBSCH (Small Business Super Clearing House)

What if I was previously using the ATO SBSCH for super payments?

The ATO is permanently removing access to the SBSCH at 11:59pm on June 30.

Before then, you need to either:

• Activate the PayDay Super integration and sign up with SuperChoice
• Or, sign up with a different (manually managed) clearing house

April–June Submissions

How should I process outstanding superannuation submissions for the April–June period?

Although PayDay Super applies from July 1, you still have until July 28 to pay the June quarter.

The ATO advises that:

• Super payments received on or before July 28 will first be applied to any outstanding June quarter amounts, with the remainder being applied to PayDay Super
• Super payments received after July 28 will be applied under the new Payday Super rules, even if you intended these payments to be made for any super you owe for the June quarter
• For more information, see Payday Super: How to manage super during the changeover on the ATO website.

The easiest way to avoid confusion and super guarantee charges is to fully pay the June quarter before processing the first payrun in the 2026–27 financial year.

Pick the payment method below that you have been using until now for options on how to pay the June quarter.

If you have already activated PayDay Super in Marlin HR, be sure to exclude any pay runs already paid through SuperChoice when making your June quarter payment.

ATO SBSCH

If you were manually entering super payments into the ATO SBSCH:

• You will not have access to the SBSCH after June 30 to make any required corrections
• The ATO therefore recommends you use your "new" superannuation solution for the Apr–Jun quarter

Using the PayDay Super Assist integration:

• Generate the Super Report for Apr–Jun as usual
• After the PayDay Super Assist integration has been set up:
  • Enter the payment info into the SuperChoice portal, instead of the SBSCH

Manual Clearing House Entry

If you were manually entering super payment info into a different super clearing house:

• Generate the Super Report for Apr–Jun as usual
• Then either:
  • Enter the payment info into the old clearing house, as usual
  • Or, Enter the payment info into the SuperChoice portal, instead of your old clearing house

Payment File Uploads

If you were creating a super payment file in HR and uploading it to a different super clearing house, you have two options.

Before activating the PayDay Super Assist integration:

• Generate the Apr–Jun super payment file as usual, and either:
  • Upload it to your existing clearing house as usual
  • Or, manually upload it to the SuperChoice portal (once set up)

After activating the PayDay Super Assist integration:

• Generate separate super payment files for each outstanding Apr–Jun pay run
• Each file will be sent to SuperChoice automatically

Sending Payment Files Manually

Usually, your payment files will be automatically generated and sent to SuperChoice whenever you finalise a pay run.

However, if SuperChoice reports errors with a submission and you are unable to correct them on the SuperChoice portal, you can correct the errors in Marlin HR and manually send a corrected submission.

SSID Numbers

If you report Single Touch Payroll (STP) through a sending service provider, you also need to notify the ATO of your sending service provider's software ID (SSID) by 30 June 2026.

Megabus will be providing your SSID number and instructions on how to upload it to the ATO portal as part of the Payday Super Assist onboarding process.

Getting Your SSID

Where can I find my SSID number?

Your SSID number will be provided to you in the Payday Super Assist Onboarding email sent to you after signing up for the integration.

If you do not sign up for the Payday Assist integration, Megabus will provide it to you separately.

SSIDs in HR

Do I have to update my SSID Number in HR?

No, you only need to update your SSID number in the ATO portal, as per the provided instructions.

Manual Super Submissions

You may need to manually generate SuperStream files to manually lodge submissions for previous pay periods, including June.

You will also need to manually generate SuperStream files if you are not using the PayDay Super Assist integration and need to upload them to another clearing house.

Payroll Emails

If you are using a different super clearing house or need to manually generate a SuperStream file for a previous period, it will be emailed to the default Email address in HR's system options.

To check the payroll email:

• Select System > Options from the menu bar
• Check the Email field at bottom-left of the System Details tab

Automatic Emailing

In order for the SuperStream file to be automatically emailed whenever a pay run is finalised, you also need to enable the Prompt to Email Super File option in System maintenance.

To enable automatic super file emailing:

• Select System > Options from the menu bar
• Click on the Banking details tab at the top
• Tick the Prompt to Email Super File checkbox

You can then upload the file to your selected clearing house.

Superannuation Report

SuperStream files for previous periods can also be generated using the Superannuation Report.

The report can be accessed by selecting Reports > Superannuation Report from the menu bar.

To generate a super file:

• Select the Payment File tab at the top
• Enter the date range
• Tick the Show pay runs already included... checkbox
• Select the required pay run(s)
• Click Generate

After the report opens:

• Click Create Payment File
• Confirm the pop-up that opens
  • If automatic emailing is enabled, the file will be sent to the payroll email
  • If not, you will need to manually retrieve the file from the specified directory on your hard drive

You can then upload the file to your selected clearing house.

Indemnification

Are we indemnified if the super is not passed on or lost once it has left our account?

Although we don't believe there to be any indemnification as such, the ATO will consider an employer's actions and intent when reviewing missed payment deadlines.

An employer can minimise the likelihood of the ATO taking action against them by performing the following tasks in a timely manner:

• Maintaining accurate details of employees and super funds in Marlin HR
• Checking the confirmation email from SuperChoice for each pay run is successful, or addressing any issues flagged on the SuperChoice portal so that the submission can be processed
• Addressing any contribution rejections by the super funds