How to Pay Employee Super in Australia — A Step-by-Step Guide for Employers

Paying employee super correctly involves more than just calculating 12% of earnings. You need to pay to the right fund, use SuperStream-compliant payment methods, meet quarterly due dates, and maintain records. This guide walks through the process from start to finish.

Step 1 — Know Your Obligation

Before making a payment, confirm:

• Who is entitled: All employees 18 or over on any OTE (ordinary time earnings), plus under-18s working more than 30 hours in a week. The $450 monthly earnings threshold was abolished 1 July 2022 — every dollar of OTE is subject to super.
• The rate: 12% of OTE from 1 July 2025 (FY2025–26)
• What counts as OTE: Regular salary, casual loading, shift allowances (for ordinary hours). Excludes overtime.
• Due dates: Contributions must reach the fund (or clearing house) by the quarterly due dates

Step 2 — Set Up Employee Fund Details

For each employee, obtain:

• Their super fund’s USI (Unique Superannuation Identifier) or ABN
• Their member account number
• Their Tax File Number (TFN) — required for SuperStream and for the fund to accept contributions without applying excess tax

New employees — fund choice process:

1. Provide a Standard Choice Form (ATO NAT 13080) within 28 days of starting
2. Wait for the employee to return the form with their fund choice
3. If no choice returned: look up their stapled fund via ATO Online Services for Business (Super > Stapled super fund)
4. If no stapled fund: use your employer default fund (must be a MySuper product)

Step 3 — Choose a Payment Method (SuperStream Compliance)

All employers must pay super via SuperStream — the mandatory electronic standard. SuperStream requires contributions to be sent with a data message (employee and contribution details) matched to a single payment.

Your options:

Option A — Small Business Super Clearing House (SBSCH)

Best for: Businesses with 19 or fewer employees, or turnover under $10 million.

• Free — operated by the ATO
• Single payment to SBSCH, which distributes to multiple funds
• Register and manage via ATO Online Services for Business
• SuperStream compliant
• Payment is deemed paid on the date you pay SBSCH (not when it reaches the fund)
• Allow 3+ business days for processing to reach funds

Option B — Payroll Software with Built-in Clearing House

Best for: Businesses using modern payroll software.

Most major payroll platforms include SuperStream-compliant clearing house functionality:

The main advantage is automation — super obligations are calculated directly from payroll data and submitted with minimal manual data entry.

Option C — Commercial Clearing House (Standalone)

For businesses not using integrated payroll software, standalone SuperStream clearing houses are available. These accept a file upload of contribution data and payment, and distribute to funds.

Option D — Direct to Fund

For some large employers with employees in a single super fund, direct payment to the fund may be possible via the fund’s employer portal. Contact the fund for their specific SuperStream data submission process.

Step 4 — Calculate Contributions

For each employee and each quarter:

1. Identify total OTE for the quarter (sum of ordinary time earnings paid in the period)
2. Apply the SG rate: OTE × 12% = contribution owing
3. Add any salary sacrifice amounts the employee has arranged (above the mandatory SG — these are separate from the 12% minimum)
4. Check for salary sacrifice adjustments: If an employee salary sacrifices additional amounts, the SG base is calculated on the OTE before salary sacrifice, unless you have explicitly reduced it (the base protection rules prevent SG from being calculated on a lower amount if it would fall below 12% of pre-sacrifice OTE)

Practical tip: Payroll software handles this automatically when configured correctly. Manual calculations should use the gross salary (before salary sacrifice) as the OTE base for SG purposes.

Step 5 — Meet Quarterly Due Dates

Contributions must be received by the fund (or the SBSCH, if using their deemed payment date) by:

Build in lead time: If paying directly to a fund (not via SBSCH), allow 2–5 business days for processing. Processing delays at the fund may cause a late payment even if you submitted on time.

If you miss a deadline, you must lodge an SGC statement and pay the SGC (Super Guarantee Charge) — which includes the contribution amount, 10% nominal interest, and a $20 admin charge per employee. SGC is not tax deductible, unlike on-time contributions.

Step 6 — Keep Records

Maintain the following records for 5 years:

• Super contribution amounts per employee per period
• The super fund paid to (fund name, USI) for each employee
• Date of payment (or SBSCH submission date)
• Employee TFN and fund membership details
• Any Standard Choice Forms returned by employees
• Records of stapled fund lookups from the ATO
• Payroll calculations used to determine OTE for each period

Records must be in English or a form readily convertible to English, and available for ATO inspection.

Step 7 — Single Touch Payroll (STP) Reporting

Super contributions are reported to the ATO via Single Touch Payroll (STP). Most payroll software automatically reports super liabilities and payments to the ATO each pay run.

Importantly, STP reports super liabilities (what you owe) and eventually the payments (what was paid). The ATO can identify employers who report liabilities but do not make corresponding payments — this is how the ATO monitors compliance.

Ensure your payroll software is STP Phase 2 compliant and that super payments are reconciled against what has been reported.

Payday Super — Preparing for 1 July 2026

From 1 July 2026, the payment frequency will change fundamentally: employers must pay super with each pay run (not quarterly). This means:

• If you run a weekly payroll, super must be paid weekly
• If you run a fortnightly payroll, super must be paid fortnightly
• The quarterly due dates will no longer apply for payday super employers

What this means for your payroll setup:

• Ensure your payroll software can submit SuperStream data with every pay run (not just at quarter-end)
• If using the SBSCH, monitor ATO announcements about how the SBSCH will adapt to payday super
• Cash flow planning: super will become a regular weekly or fortnightly cost rather than a quarterly lump sum

The ATO is expected to provide more operational guidance on payday super implementation in the lead-up to 1 July 2026.

Frequently Asked Questions

I forgot to pay super for one quarter — what should I do? Pay the outstanding super to the employee’s fund as soon as possible, then lodge an SGC statement with the ATO. The SGC statement calculates the SGC charge (which includes interest from the due date and a $20 admin fee per employee). Voluntary disclosure and prompt payment reduces penalties. Do not simply pay the late super to the fund without lodging the SGC statement — the ATO needs the statement to record the shortfall.

We process payroll fortnightly — do we pay super fortnightly or quarterly? Currently (before 1 July 2026), you pay super quarterly. You can process payroll fortnightly but accumulate the SG liability each fortnight and pay quarterly by the due dates. After 1 July 2026, payday super requires payment with each fortnightly payrun.

One of my employees has two jobs — do I still have to pay 12% SG? Yes. Your super obligation is based on the OTE you pay, regardless of how many other employers the employee has. Each employer pays their own 12% independently. There is no coordination between employers on SG.

My employee asked me to pay less super and give them more take-home pay — can I do this? No. You cannot reduce the mandatory SG below 12% of OTE regardless of what the employee requests. The SG is a legislative minimum, not a negotiable amount. An employee can make their own after-tax contributions to super, but they cannot waive their employer’s SG obligation.

See also: Employer Super Obligations. For further guidance, see the ATO’s Super for Employers resource or consult a registered tax agent.