At the end of the war, the airfield was run down and was bought back from the Air Ministry in 1957 by Edward Thomas Boyes who then farmed it with his sons until the Northern Ireland Office began work on the prison in 1976.

Mourne House, which held female prisoners, young offenders, and remands, was the first part to be opened, in March 1986.

Following the closure of HMP Belfast on 31 March 1996, Maghaberry became the adult committal prison in Northern Ireland.

In 2003, the Steele report recommended options to make Maghaberry safe, including "a degree of separation" for Irish republican and Ulster loyalist inmates.

In February 2016, a prison inspection report by the Northern Ireland Department of Justice condemned HMP Maghaberry as unsafe and unstable and lacking a correct insurance policy due to an ongoing dispute over land ownership,[3] citing suicides and clashes between inmates and prison staff.