Bookkeeping Setup for NDIS Providers (Xero/MYOB)
Set up NDIS bookkeeping in Xero or MYOB: chart of accounts, tracking categories, GST, claim reconciliation and payroll — built for prove-and-pay.
Start with the chart of accounts, not the software
Use tracking categories to tag every dollar
Get GST coding right from day one
Build reconciliation around prove-and-pay claiming
A worked example: one shift, end to end
Connect payroll properly — it is most of your cost
Watch the 90-day claim window in your ledger
Set your record retention to seven years now
Xero vs MYOB for an NDIS provider
Mistakes that cost providers real money
Your setup checklist and next step
Frequently asked questions
Is Xero or MYOB better for NDIS bookkeeping?
Neither has an NDIS-specific version — the value comes from how you configure the chart of accounts, tracking categories, GST codes and SCHADS payroll. Xero has a larger marketplace of care-sector rostering and claiming apps; MYOB's job costing suits providers running SIL across multiple houses. In practice, the rostering or claiming system you use, and your accountant's preference, usually decide it for you.
How do I record NDIS claims and payments in Xero?
Raise an invoice when you lodge a claim, crediting the relevant NDIS income account and debiting a dedicated NDIS Claims Receivable (clearing) account. When the NDIA deposit lands, reconcile it against that receivable rather than coding it straight to income. This keeps claimed-but-unpaid amounts visible, which matters under real-time prove-and-pay claiming and the proposed 90-day claim window.
Are NDIS services GST-free in my accounting software?
Most supports delivered to a participant with a plan and a written service agreement are GST-free, but not all supports are, and many of your purchases are taxable. Set NDIS income accounts to default to GST Free Income and expense accounts to GST on Expenses so you still claim input tax credits, then review edge cases individually. Confirm the current conditions against the ATO's NDIS GST guidance before applying a blanket treatment.
How should bookkeeping handle payday super and the 12% rate?
Superannuation rose to 12% from 1 July 2026, and payday super requires paying super at the same time as wages rather than quarterly. In Xero or MYOB, set your super clearing-house arrangement so super leaves your account each pay run, and map each SCHADS pay item to the correct wage and superannuation accounts. Confirm commencement timing and any transitional rules against ATO guidance.
How long do NDIS providers need to keep records?
A seven-year record-retention duty is proposed in the 2026 reform Bill and is not yet law, but seven years already aligns with ATO expectations, so default to it. Keep source evidence — service agreements, timesheets, claim evidence — retrievable and linked to the matching ledger transaction. Under prove-and-pay, evidence is captured at the point of claim, so file it in a way an auditor can trace back from your books.