In the mid-1990s, Mosab Hassan Yousef decided to accept a Shin Bet offer to become an informant after witnessing Hamas inmates leading a brutal year-long campaign at the prison to weed out supposed Israeli collaborators, using techniques such as torture and murder.

In January 2005, soldiers serving in the prison were accused of selling about 150 mobile phones to security detainees.

On 23 February 2013, Arafat Jaradat, a 30-year-old Palestinian who had been arrested by the Shin Bet 5 days earlier died in the Megiddo Prison.

Since the outbreak of the war, Palestinian detainees, as well as those with Israeli citizenship, reported in numerous cases being subject to humiliation, starvation, medical neglect, violence and torture.

[6][4] At the end of 2005, as part of an archaeological dig at the Legio site on the depopulated Palestinian village of Lajjun, which is within the prison's boundaries, a mosaic and the remains of a building were found, which are apparently the oldest church in the world.