Merna Aprem, a 20-year-old with epilepsy and autism, drowned in the bath of her NDIS-funded residential home in Woodbine on May 23, 2019.
Support workers discovered her face down and surrounded by vomit.
Ms Aprem moved into the group home, managed by the Australian Foundation for Disability (Afford), two months before her death.
Afford chief executive Joanne Toohey appeared before the disability royal commission last week.
She was quizzed about a broad range of safety and training recommendations from the commission's report, which will be publicly released in September.
One week on from the appearance, Afford announced three of its directors had resigned.
"Afford takes full responsibility and accountability for the failings identified by the Royal Commission into Violence, Abuse, Neglect and Exploitation of People with Disability Royal Commission – from 2015 to 2021," the provider said in a statement on Thursday.
"The Afford of today is uncompromising in our commitment to safeguarding our clients and ensuring rights-led client choices and practice."
The company thanked the directors for their "considerable service".
Submissions about Ms Aprem's death were made to the royal commission by the Autism Advisory and Support Service, who helped her secure National Disability Insurance Scheme funding before she moved into the Woodbine group home.
"I hope the royal commission will ensure positive changes are made where it comes to the care of our vulnerable," the service's Grace Fava told AAP at the time.
In December 2019, the national disability services watchdog took the unprecedented step of suing Afford over Ms Aprem's death, accusing the provider of a litany of failures.
In documents filed in the Federal Court, the watchdog alleged the company failed in its obligations to support Ms Aprem in a safe and competent manner, leaving the 20-year-old at "real and significant risk".
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