Human rights organizations and prisoners have reported human rights abuses against
Palestinian prisoners in the facility, particularly following the
events of October 7, 2023. Reports have cited systematic torture, violence, medical neglect, and inadequate living conditions. In September 2024 photos and videos revealed Israeli security guards mistreating Palestinian prisoners at 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. An unnamed senior Israeli Prisons Service official acknowledged to the media that there is "severe violence" against prisoners, while the service described procedures as "routine". On 24 March 2025, it was reported that 17 year-old Palestinian prisoner Walid Khaled Abdullah Ahmad had died in unknown circumstances in Megiddo. The Palestinian Prisoners Club
NGO stated he was the 63rd Palestinian to die in an Israeli jail since the beginning of the
Gaza war. It was later discovered that he died from signs of "starvation, dehydration from colitis-induced diarrhea, and infectious complications all compounded by prolonged malnutrition and denial of life saving medical intervention", according to the
Defense for Children International – Palestine. == Megiddo church and mosaic ==