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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…

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…

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,…

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…

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…

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