They were remanded on bail until sentencing on October 25.
Serious Fraud Office director, Julie Read, said the Ellenbroeks' offending took place over a sustained period, was premeditated and the amount of public funds stolen was significant.
"The funds were allocated for community day care and vocational services for people with intellectual disabilities. The offending came at the expense of some of the most vulnerable members of our society, with whose care the Ellenbroeks were entrusted," she said.
Alpha's client base included individuals with mild to challenging intellectual disabilities and enabled them to participate in activities such as music, reading, puzzles, sports, baking, and offsite community-based activities.
The trust received funding from both the Ministry of Health and the Ministry of Social Development, as well as donations and funding grants from other sources.
It ceased operation in February 2015 after 17 years of operation.
The Serious Fraud Office is the lead law enforcement agency for investigating and prosecuting serious or complex financial crime, including bribery and corruption.