How does STP Phase 2 affect NDIS payroll?

Under STP Phase 2, employers must disaggregate gross, report income types and country codes where relevant, and separately map allowances and paid leave types. Your payroll system must be configured to correctly map these categories before lodging to the ATO.

Do I pay super on allowances and overtime?

Superannuation generally applies to ordinary time earnings. Some allowances are OTE while others are not. Overtime is typically not OTE. Check ATO guidance and ensure each pay item is flagged correctly in your payroll software to avoid super shortfalls.

How do I handle travel time and mileage between clients?

Under SCHADS and your policies, you may need to pay travel time between clients and reimburse vehicle expenses (for example a cents-per-km allowance). Configure timesheets and payroll with distinct categories for travel time and mileage, and set the appropriate tax, super and STP treatment.

What onboarding documents do NDIS providers need for payroll?

Collect a TFN declaration, super choice form, right-to-work documents where relevant, bank details, emergency contacts, and NDIS Worker Screening clearance. Depending on the role you may also require Working With Children Checks and current police checks.

What state-based obligations might apply?

Some jurisdictions have portable long service leave schemes for community services (for example, VIC, ACT and QLD). NDIS providers should confirm whether they must register and report. You may also have payroll tax obligations depending on your wage bill and state thresholds.

NDIS Provider Accountant | Payroll Help for NDIS Provider

Q: Which award usually applies to NDIS support workers?

Most frontline NDIS roles fall under the SCHADS Award. Some providers also employ nurses under the Nurses Award. Correct classification, minimum engagement rules, penalty rates, broken shifts, sleepovers and allowances must be set up accurately in payroll.

How payroll services for NDIS providers usually work

Strong NDIS payroll support starts with a short discovery: your award coverage, classifications and pay rules, the software you use, roster patterns, current pain points and any ATO or Fair Work deadlines.

Work then splits into three layers:

Immediate triage: correct urgent issues (missed super, STP errors, wrong allowances, underpayments/overpayments).
Design and build: set up pay calendars, earnings and allowance categories, leave rules, super, STP Phase 2 mapping and integrations with your rostering system.
Ongoing pay runs: validate timesheets, review exceptions, publish payslips, lodge STP, reconcile super and leave balances, and maintain a compliance calendar.

Talk to an NDIS payroll specialist

Australian context to keep in view

PAYG withholding registration is required before withholding from employees and some contractors.
Single Touch Payroll (STP) Phase 2 requires disaggregated reporting and correct mapping of income types, allowances and leave.
The Super Guarantee rate increased to 11.5% from 1 July 2024; pay super by quarterly due dates to avoid the Superannuation Guarantee Charge.
Fair Work compliance: SCHADS minimum engagement, broken shifts, sleepovers, penalties and allowances must be implemented correctly in payroll.
Portable long service leave can apply to community services in VIC, ACT and QLD—check registration and reporting obligations.

Common software used by NDIS providers includes Xero Payroll, Employment Hero/KeyPay, MYOB and QuickBooks, along with rostering and care management tools such as ShiftCare, Deputy and Tanda.

What to compare before you commit

Scope

Confirm the proposal covers award interpretation, pay item setup, leave rules, super configuration, STP Phase 2 mapping, integration with your rostering tool, and ongoing pay runs with exception handling.

Software fit

Ask for demonstrated experience with your stack (e.g. Xero + ShiftCare, KeyPay + Deputy). Request examples of correct mapping for sleepovers, travel time and km allowances.

Turnaround and communication

Clarify cut‑offs for timesheets, approval workflows, escalation for urgent issues and who signs off on award changes or back‑pay decisions.

Commercial fit

Understand pricing (per employee, per pay run or fixed fee), what’s included (STP lodgements, super payments, end‑of‑year finalisation), and any fees for cleanup or Fair Work reviews.

Get a tailored NDIS payroll plan

NDIS payroll compliance checklist

Confirm award coverage and level for each role (SCHADS/Nurses) and document in employee records.
Create distinct pay items for penalties, broken shifts, sleepovers, travel time, km allowances and first aid/meal allowances.
Flag each pay item for tax, super and STP correctly (OTE vs non‑OTE, allowance types, leave categories).
Enable STP Phase 2 and verify mapping with a test lodgement before the first live pay cycle.
Integrate your rostering tool and set tolerance rules for timesheet variances and approvals.
Set a compliance calendar: super due dates, STP finalisation, award rate changes and public holiday rules.
Run periodic payroll audits to catch leave accrual anomalies, negative balances and inactive employees.

Request a payroll compliance review

Software and integrations we support

We work with leading Australian payroll and rostering solutions used by NDIS providers:

Payroll: Xero Payroll, Employment Hero/KeyPay, MYOB, QuickBooks Payroll
Rostering and care: ShiftCare, Deputy, Tanda
Super clearing and STP: ATO‑enabled STP tools, SuperStream‑compliant gateways

The goal is a clean data flow: rosters to timesheets to payroll to STP and super—without manual re‑entry.

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Common NDIS payroll pitfalls we fix

Sleepover and broken shift rules not configured, causing underpayments or overpayments.
Travel time and km reimbursements miscoded, affecting tax, super and STP treatment.
Incorrect leave accruals for part‑timers and casuals, including public holiday handling.
Super not paid on time or calculated on the wrong base, risking penalties.
STP Phase 2 mapping errors leading to ATO rejections or year‑end mismatches.
Rostering integrations duplicating or dropping timesheets due to mapping gaps.

Best next steps

List your roles, awards and problem areas (for example: travel time not paid, sleepovers inconsistent, STP errors, super late, roster not syncing). Decide whether you want a full rebuild, a compliance review, or ongoing pay run support.

Then compare providers against your exact outcomes—accurate awards, timely pay runs, fewer manual steps, clear reporting—not just titles. Ask for examples of their NDIS payroll mapping and audit approach.

Start my NDIS payroll setup

Use these related pages to explore connected topics:

Frequently asked questions

Which award usually applies to NDIS support workers?

Most frontline NDIS roles are covered by the SCHADS Award. Some providers also employ nursing staff under the Nurses Award. Correct classification and pay rules for penalties, broken shifts, sleepovers and allowances need to be reflected accurately in payroll.

How does STP Phase 2 change my obligations?

STP Phase 2 requires disaggregated reporting and correct mapping of income types, allowances and leave. Your payroll must be configured to categorise each earning and allowance correctly before lodging to the ATO.

What about travel time and mileage between clients?

Depending on your policies and the SCHADS Award, travel time between clients may be payable and vehicle expenses reimbursed (e.g. a cents‑per‑km allowance). Configure separate pay items and ensure tax, super and STP treatment is correct.

Do I owe super on allowances or overtime?

Super generally applies to ordinary time earnings. Some allowances are OTE while others are not; overtime is typically not OTE. Each pay item should be flagged correctly in your software based on ATO guidance.

Are there portable long service schemes for NDIS providers?

Yes, community services in VIC, ACT and QLD have portable long service schemes. Check whether your organisation must register and report in your state.

Which tools work best for NDIS payroll?

Common setups include Xero Payroll or KeyPay/Employment Hero paired with ShiftCare, Deputy or Tanda for rostering. What matters most is correct award mapping and a clean integration from roster to payroll to STP and super.

Get answers for your situation

Payroll Services for NDIS Providers