Selling or Buying an NDIS Business in 2026: What CGT and GST Mean for Your Bottom Line
Most NDIS business sellers know roughly what their business is worth. Far fewer know what they will actually keep after tax. And most NDIS business buyers do not realise the way a deal is structured can change both the price they pay and the risk they inherit.
If you plan to sell NDIS business assets or buy NDIS business operations this year, tax deserves a seat at the table from day one, not after the contract is signed.
Why Tax Matters More in 2026
The regulatory side of the Australian NDIS business market has tightened. From 1 July 2026, providers must notify the NDIS Commission as soon as possible after they know a change of ownership will happen, and some providers face a new change-of-ownership audit. That affects when you sign, when you settle and when tax events occur.
NDIS business valuation is no longer just a multiple of earnings. Buyers price in compliance history, audit risk and tax structure, and sellers who understand this negotiate from a stronger position.
Step One: Share Sale or Asset Sale?
This is the first decision, and it shapes almost everything else. Our guide to share sales versus asset sales for NDIS businesses explains the practical differences in more detail.
- Share sale: the buyer takes over the company, including its NDIS provider registration, contracts, history and liabilities.
- Asset sale: the buyer acquires selected assets, such as goodwill, participant relationships and equipment, into their own entity.
NDIS registration is tied to the legal entity, so buyers who want a registered NDIS provider for sale usually need to buy the entity itself. An asset sale can suit a buyer who is already registered, but the Commission’s change-of-ownership guidance still applies to a sale or transfer of all or part of a business. Confirm the structure with your solicitor and accountant before going to market.
Structure also drives tax. Sellers and buyers often prefer different outcomes, and this is where specialist NDIS business brokers help both sides reach a workable middle.
CGT Concessions: The Part Sellers Often Miss
Capital gains tax (CGT) usually applies to the gain when you sell goodwill or shares. The ATO’s small business CGT concessions can reduce, disregard or defer part of that gain, but only if you meet the basic conditions first. Broadly, these include:
- being a small business entity, or passing the $6 million maximum net asset value test
- the asset being an active asset used in the business
- extra tests if you are selling shares in a company or units in a trust
There are four concessions:
- 15-year exemption: a full exemption if you have owned the asset continuously for 15 years and are 55 or older and retiring, or are permanently incapacitated.
- 50% active asset reduction: halves the gain and applies automatically if the basic conditions are met, unless you choose otherwise.
- Retirement exemption: disregards gains up to a $500,000 lifetime limit.
- Rollover: defers the gain for at least two years while you acquire a replacement asset.
Many NDIS owners have built their business in under 15 years, so the 50% reduction and retirement exemption are often the relevant ones. Who counts towards the $6 million test can catch people out, so model your position 12 to 24 months before selling.
GST and the Going Concern Exemption
If a business is sold as a going concern, the sale can be GST-free. Under the ATO going-concern rules:
- the sale is for payment
- the buyer is registered, or required to be registered, for GST
- both parties agree in writing that it is a going concern, on or before the day of supply
- the seller supplies everything necessary to keep operating the business
Here is the NDIS twist. Many disability supports are GST-free, so some owners assume GST never applies to them. But the going-concern rules depend on registration status, and the seller generally needs to be registered, or required to be, too. Check yours with your accountant.
Contracts should also include a fallback clause. If the ATO decides the sale was not a going concern, the seller must remit the GST, so sellers should seek an indemnity from the buyer. Buyers benefit too: a going-concern sale can reduce upfront cash needs and, in some states, stamp duty.
What Buyers Should Check
Good NDIS provider due diligence goes beyond the Commission’s register. Check the tax position too:
- BAS, PAYG withholding and super lodgements are up to date
- there are no unresolved ATO debts or payment plans
- staff entitlements are accurately recorded and priced into the deal
- NDIS compliance, audit history and worker screening are in order
In a share sale, hidden tax liabilities become the buyer’s problem on settlement day, so warranties and indemnities matter.
A Simple Seller’s Checklist
- Check CGT concession eligibility with an accountant well before listing.
- Settle structure with your solicitor before approaching buyers.
- Confirm your GST registration and going-concern eligibility.
- Bring NDIS compliance documentation up to date.
- Align Commission notification timing with the contract timeline.
This article provides general information only and is not tax, legal or financial advice. Speak to a qualified accountant or solicitor about your circumstances.
Talk to NDIS Business Brokers Before You Sign
Whether you want to sell, buy or simply understand your options, our team works exclusively in this sector. We help sellers prepare, price and position their business, and we help buyers find the right NDIS business for sale and move through due diligence with confidence. Contact us for a confidential discussion.
