Payroll

The Payroll page manages your entire pay run lifecycle — from creating pay runs through to paying employees, lodging with the ATO, and sending payslips.

Finding Pay & Lodge and STP: Open Team → Payroll, then open a pay run to its detail page. Pay & Lodge (wages, super, and ATO Reporting (STP)) is on that pay run — not only on the period list.

STP finalisation status (read-only): Open Team → STP to see each employee’s year-end STP finalisation status for the current and prior financial year (informational only; lodging is still from Pay & Lodge on each pay run).

STP Phase 2 (V1) — what the product supports

Employee STP income types are SAW (Salary and Wages), CHP (Closely Held Payees), WHM (Working Holiday Makers), and SWP (Seasonal Worker Programme). WHM requires a two-letter income stream country code. Reporting components covered in the product include RESC (Reportable Employer Super Contributions), child support (deduction and garnishee lines), RFBA (Reportable Fringe Benefits Amount) on the pay item, prior payroll BMS / Payroll ID (Team → Payroll settings) for migrations, and missed pay events (lodge from Pay & Lodge when a run was not reported on pay day). Use STP Update in Pay & Lodge only to correct an event the ATO has already accepted.

Overview cards

Summary cards at the top of the page show your current pay run status:

Pay periods

Navigation

Use the period navigation to move between pay cycles:

• Previous Period — go back to earlier pay periods
• Current Period — jump to today’s date range
• Next Period — move forward (disabled if already at latest)

The display shows the start date, end date, and highlights whether you’re viewing the current period.

Unscheduled pay runs

For payments outside normal cycles (bonuses, corrections, terminations), click Unscheduled Pay Run to create a one-off pay run with custom dates.

Pay run workflow

Each pay run moves through a structured lifecycle:

Draft → Approved → Processed → Pay & Lodge → Complete

1. Draft

• System creates a pay run for each pay period
• Employees are populated from timesheets and salary defaults
• If an employee has Standard Pay configured, recurring allowances, deductions, salary sacrifice, and RESC are pre-filled automatically into their pay item with correct gross, tax, and net figures
• Review hours, rates, and calculations
• Make adjustments as needed

Allowances in the pay run editor

Each allowance line has an STP type (e.g. CD — cents per km, LD — laundry, MD — overtime meal, KN — task, QN — qualifications, OD — other), a dollar amount, and a checkbox directly underneath:

Include in super calculation — Leave ticked unless this line is a genuine expense reimbursement (e.g. cents-per-km at the ATO reasonable rate) that your award does not count toward super.

• Default: ticked. The line is included in the super calculation base for that pay run.
• Untick it only when the allowance is a pure expense reimbursement that your modern award does not count toward super.

Whether an allowance counts toward super is set by Australian super law, not by the STP code. See Allowances and super for the compliance rules, the STP types that are usually expense reimbursements (CD, LD, MD, RD, TD), and the “all-purpose” award caveat.

Important: Unticking this box only changes the super calculation. It does not change the STP code reported to the ATO, the gross pay amount on the payslip, or PAYG withholding — the allowance still appears at its full amount on the payslip and in STP.

If you’re unsure, leave it ticked. Overpaying super by a small amount is recoverable; underpaying creates a Super Guarantee shortfall and ATO penalties.

2. Approved

• Submit the draft for approval
• An authorized user reviews all employee entries
• Checks hours, rates, tax, and superannuation calculations
• Approves to proceed to processing

3. Processed

• Processing creates the accounting journals for wages and super
• Super payment records are created for each employee
• Leave accruals are calculated
• The pay run is now ready for payment

4. Pay & Lodge

This is where you pay your employees and lodge with the ATO. The Pay & Lodge page is a payment summary dashboard that brings everything together in one place.

Wages card

Shows each employee’s net pay amount and a running total. Expand the Payment Details section to see employee bank details (BSB, account number, account name) so you can verify where payments are going.

Superannuation card

Shows super contributions grouped by fund, with employee counts per fund and total super amount. The Payment Details section expands to show fund BSB, account number, and payment reference numbers.

If SuperStream is configured, the card shows the current submission status.

Make Payment section

Below the two summary cards, the Make Payment section provides:

• Download ABA File (optional) — generates a bank file containing all wage payments. Upload this to your internet banking to pay everyone in one batch transfer.
• Mark as Paid — confirms you’ve arranged payment for wages. This records the payment, creates the wage payment journal entry, and deducts leave balances.

You don’t need to use the ABA file — if you prefer to pay employees individually through your bank, simply review the payment details and click Mark as Paid when done.

ATO Reporting (STP)

After wages are marked as paid, the STP section appears on Pay & Lodge. Single Touch Payroll reports your payroll data to the Australian Taxation Office.

• Use Submit original STP event for the first accepted lodgement for that pay run
• Use STP Update only when correcting a pay run that has already been accepted by the ATO
• The system generates the required XML and submits via the Ozedi gateway (configured for your environment)
• Status updates when you refresh or poll: e.g. submitted → processing → accepted
• If rejected, review the error details, fix data (e.g. TFN, address, tax settings — see Team Members → TFN for valid TFN values and exemption rules), and Retry Submission

Submit vs STP Update

Rebased separates the two STP actions so operators can choose the right lodgement mode:

Important: STP Update is not a general “resend” button. It is used only after there is already an accepted STP submission for that pay run.

EOFY — wrapping up a financial year with the ATO

After you’ve processed the last pay run for a financial year, you tell the ATO the year is done for your employees. This is called EOFY finalisation — it confirms to the ATO that each employee’s year-to-date figures are complete, so their income can pre-fill in their myGov tax return.

Where to do it: Team → STP. This is a one-click flow — no pay run required.

When to do it: Once all pays for the year have been processed. This is typically July or later. The ATO’s deadline is 14 July after year-end, but there’s no penalty for being a bit late — finalise as soon as you’re confident the year is complete.

How it works:

• Open Team → STP. You’ll see both the closed and current FY as columns.
• Click Finalise on each employee, or Finalise all N for FY 20XX-XX to do the whole column at once.
• The ATO receives each employee’s cumulative year-to-date totals from every pay run in the year — not just one particular run.
• No wages, tax, or super are paid. This is purely a finalisation event.
• Each row flips from Finalise → Submitted → Finalised as the ATO acknowledges it.

If you need to re-send a finalisation (e.g. YTD figures were corrected, a late adjustment pay was processed, or the ATO asked you to resend): hover over the Finalised pill and click the small ↻ Re-finalise link. Provide a reason; the new event replaces the old one at the ATO (“last event wins”).

If the ATO rejects a finalisation: the cell shows a Retry button with the rejection reason on hover. Fix whatever the ATO flagged (usually an employee profile issue — missing address, wrong TFN, etc.) and click Retry.

See the STP Overview page for the full walkthrough.

Final pay on termination

When an employee leaves, their last pay is handled via the Terminate Employee flow:

1. Go to Team → Team Members and open the employee’s profile
2. Click Terminate Employee and fill in the termination details
3. Select Yes for “Final pay in Rebased?” and choose the draft pay run for their final pay
4. After termination, open that pay run and edit the employee’s pay item
5. In the Termination Leave Payout section (visible when final pay is ticked), review the auto-populated leave balances
6. Annual Leave and Long Service Leave are calculated with the employee’s ordinary rate (plus 17.5% leave loading for Annual Leave)
7. Adjust if needed, then save
8. Process the pay run and lodge STP as normal

The leave payout is:

• Reported as Paid Leave Type U (unused leave on termination) in STP
• Excluded from superannuation — it’s not ordinary time earnings
• Taxed using the ATO’s marginal rate method (Method B(ii) from NAT 3348)

See Team Members for the full termination workflow.

Note: The Payroll list may show an ATO Reporting (STP) banner such as “Not connected”. That panel is informational. Lodging STP is done per pay run from Pay & Lodge after wages are marked paid, when Ozedi STP is enabled for your business.

Typical user flow

1. Review employee amounts on the Wages and Super cards
2. Expand Payment Details to verify bank accounts if needed
3. Download the ABA file (optional — for batch bank payment)
4. Click Mark as Paid
5. Lodge STP from the ATO Reporting (STP) section:
   • Submit original STP event for the first lodgement
   • STP Update only if correcting an already accepted event
6. Proceed to Payslips

5. Payslips

After completing Pay & Lodge, send payslips to employees:

• Generate PDF payslips for each employee
• Email payslips individually or in bulk
• Employees can also access payslips through their self-service portal

ABA files

What is an ABA file?

An ABA (Australian Bankers’ Association) file is a standard format used by Australian banks for batch payments. Instead of paying each employee individually, you upload one file to your internet banking and all payments are processed together.

Setting up ABA

Before you can download ABA files, configure your bank details in Team > Settings > Payment Settings:

If ABA is not configured, the Download ABA File button won’t appear — you’ll see a prompt to set it up in Settings instead.

Employee bank details

For ABA files to work, employees need bank details on file (BSB, account number, account name). These are configured in each employee’s profile under Team Members. Employees missing bank details are skipped from the ABA file and shown with a dash in the Payment Details table.

Pay run statuses

Superannuation in Pay & Lodge

Super contributions are shown alongside wages on the Pay & Lodge page. This design supports Payday Super compliance (effective 1 July 2026), which requires super to be paid within 7 days of payday.

Payday Super reminders

When wages are paid but super is still pending, the system shows reminders:

These reminders also appear on the Payroll dashboard and the main Dashboard.

AU-specific considerations

Tax calculation (PAYG)

• PAYG withholding tax is calculated automatically using ATO tax tables
• Considers the tax-free threshold election
• Accounts for HELP/HECS debt repayments
• Updated when ATO publishes new tax tables

Superannuation Guarantee (SG)

• Current rate: 12% (2025–26, the final legislated rate)
• Calculated automatically each pay run on what counts toward super
• Applied to regular wages, salaries, commissions, and most allowances
• Overtime and genuine expense reimbursements are excluded — see Superannuation → Allowances and super for how each allowance line is handled

STP compliance

• Mandatory for all Australian employers
• Reports gross pay, PAYG tax, and super each pay run
• Submitted to ATO via the Ozedi gateway
• ATO receives data in real time after each pay run
• Supports original submissions, updates/amendments, EOFY finalisation workflows, and final-pay scenarios

Fair Work

• Minimum wage and award rates
• Penalty rates for overtime, weekends, and public holidays
• Leave loading where applicable

Reverting a pay run

If you need to make corrections after processing, click Revert to Draft on the Pay & Lodge page. This:

• Deletes the payroll journal entries
• Removes super payment records
• Reverses leave accruals
• Returns the pay run to draft status for editing

For corrections after a pay run is completed, see Pay Corrections below.

Pay corrections

Underpayment (top-up)

If an employee was underpaid (e.g. you entered too few hours), you have two options:

1. Unscheduled pay run — click Unscheduled Pay Run from the payroll list, create the run, then remove all employees except the affected one. Enter the missing hours or amount. Standard tax and super calculations apply automatically.
2. Next scheduled pay run — add the extra hours or amount to the employee’s next regular pay run.

Overpayment (recovery)

If an employee was overpaid, reduce their hours or amounts on the next scheduled pay run:

• Hourly employees — reduce ordinary hours or overtime hours (e.g. paid 46 hours instead of 45, enter 44 hours next run)
• Salary employees — use the One-off Salary Adjustment field in the pay item editor with a negative amount (e.g. -$200)
• Allowances — enter a negative allowance line if an allowance was overpaid

Do not use an unscheduled pay run for overpayment recovery. Corrections must be applied within a regular pay run.

Important rules

• Gross pay cannot go below zero for any employee. If the overpayment exceeds one pay period, split the correction across multiple pay runs.
• Tax (PAYG) and super are automatically recalculated when you reduce the gross — no manual adjustment needed.
• STP year-to-date amounts decrease automatically on the next lodgement. No separate STP Update is required.

Examples

Best practices

Before processing

• Review and approve all timesheets
• Check leave taken during the period
• Verify new employee rates and start dates
• Update any terminations

Accuracy checks

• Compare totals to the previous pay run
• Check for unusual variances
• Verify hours match approved timesheets
• Confirm tax and super rates are current

Timing

• Process before the scheduled payment date
• Allow time for approval review
• Consider bank processing times (ABA files typically settle next business day)
• Account for weekends and public holidays

Troubleshooting

Pay run won’t create

• Check the pay period hasn’t already been processed
• Verify your user account has payroll permissions
• Ensure at least one employee is active for the period

Wrong calculations

• Verify tax tables are current (check Settings)
• Review employee tax settings (tax-free threshold, STSL / study and training loan)
• Confirm the super rate matches current SG legislation
• Check timesheet hours imported correctly

”TFN or exemption is required” on approval

Rebased blocks pay-run approval if any included employee has no TFN value and no TFN exemption on file. To fix:

1. Open the employee from Team → Team Members → Pay & Tax.
2. Enter either a real 9-digit TFN, the ATO placeholder 111 111 111 (employee has applied for a TFN — valid for 28 days), or 000 000 000 (employee has not supplied a TFN — triggers 47% withholding).
3. Or record a TFN exemption (pension / under 18 / payee declaration) if the employee qualifies.
4. Return to the pay run and approve again.

See Team Members — Tax File Number for the full reference including the 28-day rule.

STP submission failed

• Verify your business ABN is correct in Settings
• Check the Ozedi STP connection is active
• Ensure the pay run status is wages_paid or completed
• Review any ATO error codes in the submission details
• If the earlier lodgement was not accepted, retry the original submission instead of sending an STP Update

EOFY finalisation reminder appears

• The reminder means EOFY wrap-up may still be due for the financial year shown.
• Click the banner link to jump to Team → STP, where finalisation is a one-click action per employee (or in bulk per FY).
• Finalise once all pays for the year have been processed (typically July or later).
• See STP Overview for the full walkthrough, re-finalisation, and retry-after-rejection.

ABA file issues

• Confirm ABA bank details are configured in Settings
• Check all employees have valid BSB and account numbers
• Verify the business bank account details are correct

Mark as Paid not working

• Ensure the pay run is in processed status
• Check for any existing payment records that may conflict
• Try refreshing the page and retrying

Related pages

• Team → STP (in the app) — read-only year-end STP finalisation status per employee (see intro above)
• Standard Pay — set up recurring allowances, deductions, salary sacrifice, and RESC per employee
• Timesheets — hours feed into payroll calculations
• Superannuation — fund management and contribution history
• Team Members — employee profiles and bank details
• Settings — pay cycle, ABA bank setup, leave/timesheet prefs; STP is lodged from Pay & Lodge (see above)
• Leave — leave balances and accruals