Tax and accounting for NDIS plan managers.
Running a plan management business means handling participant funds you don't own, so your accounting needs the same reconciliation discipline as any business holding client money, on top of the usual GST and structure questions every provider faces. This guide covers what plan managers typically claim, how GST applies to your management fee, and why segregating and reconciling participant funds properly is the backbone of a plan management business. We're Brisbane based and work with plan managers across Australia.
Updated July 2026 · Reviewed by the LINK Advisors team
What plan managers can claim.
Ordered by typical value. Every claim still has to pass the ATO's tests: you paid for it, it relates to earning your income, and you can show a record.
Plan management platform software
Subscriptions to claiming, invoicing and reconciliation software built for plan management are generally deductible.
Professional indemnity insurance
Cover for your role handling participant funds is generally deductible, and worth carrying given the responsibility involved.
Worker screening checks
Screening checks for staff processing claims are generally deductible.
Staff wages for claims processing
Wages paid to your claims processing team are generally deductible business costs.
Accounting and audit fees
Fees for the reconciliation and audit support that keeps participant fund handling compliant are generally deductible.
Bank fees on high transaction volumes
Fees associated with the volume of participant transactions your business processes are generally deductible.
Office and admin costs
Running costs for the office space your claims team operates from are generally deductible.
Professional association membership
Membership fees for relevant plan management bodies are generally deductible.
Marketing and referral partnerships
Costs of building referral relationships with support coordinators and providers are generally deductible.
Training on pricing arrangements and claiming rules
Staff training to keep claiming practices current is generally deductible.
GST-free, if the paperwork holds.
Plan management is generally GST-free where it's provided as a support under a participant's plan, with the plan and agreement requirements met, in the same way as other NDIS supports. The fee you charge for managing a participant's funds sits under that same general rule, though it's worth confirming your specific fee structure against current guidance rather than assuming every part of your billing automatically qualifies.
Where you're passing through payments to other providers on a participant's behalf, that flow of funds needs to be kept clearly separate from your own management fee in your accounting, both for GST purposes and so participant money is never mixed with revenue that's actually yours.
Getting this split right in your invoicing and Xero tax codes matters more as claim volumes grow, since a small error repeated across hundreds of participant transactions becomes a real reconciliation problem rather than a one-off fix.
The right structure for the work.
The core discipline in plan management is trust-like handling of participant funds: money that belongs to participants and providers needs to sit clearly separate from your own business account, with reconciliation tight enough that you could account for every dollar at any point. Most plan management businesses operate as companies given the scale, staffing and NDIS Commission registration requirements involved, and we build your chart of accounts and bank feeds specifically around keeping participant funds and business revenue visibly apart, not just theoretically separate.
Run the work, we run the numbers.
Plan management platforms handle claiming against the NDIA portal and provider invoicing, and connecting that properly to Xero means your own management fee income is tracked separately from the participant funds flowing through your business. We set up daily reconciliation between your plan management platform and Xero so nothing sits unreconciled for long enough to become a real problem at audit time.
Frequently asked questions.
Is plan management GST-free?
Generally yes, under the same plan-and-agreement rules that apply to other NDIS supports, though it's worth confirming your specific fee structure with us.
How do I keep participant funds separate from my own business account?
Through disciplined segregation and daily reconciliation, ideally with a chart of accounts and bank feed structure built specifically for that purpose. We set this up rather than relying on manual tracking.
What records do I need for an NDIS Commission audit?
Clear reconciliation records, service agreements and claim logs that show participant funds have been handled correctly. We keep these current as part of your regular bookkeeping rather than reconstructed at audit time.
Should a plan management business be a company?
Generally yes, given the scale, staffing and registration requirements most plan management businesses carry.
Do I need to register as an NDIS provider to offer plan management?
Registration requirements apply depending on how you operate, and we can help you work out what's needed before you take on participants.
Talk to an accountant who knows plan manager businesses.
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