The organisation employs 3,000 staff and volunteers in 300 locations across Kildare, Wicklow, Dublin, Meath, Louth and Kerry.
St John of God Community Services will not transfer to the HSE after an agreement was reached on funding.
8,000 children and adults receiving intellectual disability and mental health services will continue to do so as currently provided.
The HSE and St John of God Community Services held intensive discussions over funding, and also agreed a timeline for final decisions relating to an historical deficit.
The organisation employs 3,000 staff and volunteers in 300 locations across Kildare, Wicklow, Dublin, Meath, Louth and Kerry.

Staff Say Unsafe Pressure At Naas Hospital Is Worsened By Uncovered Sick Leave And Vacant Positions
Inside The Celbridge Lab Where Evidence Helped Identify 32 Missing People Last Year
Man Assaulted By Two Males In Newbridge After Refusing To Hand Over His Jacket
Taoiseach Says Patients Shouldn’t Pay for Blister Packs - But Says State Can't Pay For Everything
Council Executive Asked Naas Cllrs To Refuse Free Xmas Parking To Encourage Use Of "Sustainable" Travel
Gunman Steals Cash From Centra In Naas Before Being Tracked Down By Gardai
Woman Arrested At Dublin Airport Detained In Kildare Garda Station Over Alleged Series Of Thefts
Vulnerable People And Those With Disabilities In Kildare Left Waiting A Year For Basic Advocacy Support