Islam was accused of being a commander of Al-Badr's Rangpur branch during the 1971 Bangladesh Liberation War. ^[15] Al-Badr was a militia that collaborated with Pakistani forces during the war and was involved in the Bangladesh genocide. ^[16]

On 22 August 2012, Islam was arrested in Maghbazar. ^[17] The International Crimes Tribunal (ICT) filed five charges of crimes against humanity, including accusations of genocide, murder, and abduction. ^[18] At the time, he was serving as the assistant general secretary of Jamaat-e-Islami. ^[19] His prosecutor at the trial was Nurjahan Begum Mukta. ^[20] His defence team was composed of senior counsel Abdur Razzaq, Mohammad Shishir Manir, and Imran Siddique. He was accused of involvement in the Jharuarbeel massacre, in which more than 1,200 Hindus were murdered, a pregnant woman was raped at Rangpur Town Hall, and a Mukti Bahini member and his brother were tortured. ^{[21] [22] [23]} A woman testified that he was involved in the rape of a pregnant woman for 19 days at Rangpur Town Hall during the war. ^{[15] [24] [25]}

In December 2014, he was convicted of war crimes and sentenced to death by the ICT. ^{[26] [27]} He was acquitted of the murder of ten people in Rangpur but was convicted of rape at the Rangpur Town Hall and torturing the Mukti Bahini member and his brother at an Al-Badr camp. ^[26] The three-member tribunal was led by Justice M Enayetur Rahim and included Justice Jahangir Hossain and Justice Anwarul Haque. ^[26] His reaction after the verdict was, "... Allah will try you, Insha'Allah ". ^[26] Jamaat-e-Islami called for a two-day strike (hartal) following the verdict. ^{[26] [28]}

Islam's defence argued that the charges were politically motivated, but his appeals were rejected by the Supreme Court of Bangladesh in 2019. ^[29] The Appellate Division bench was led by Chief Justice Syed Mahmud Hossain. ^[30] Islam's principal lawyer at the appeal was Khandaker Mahbub Hossain, a politician of the Bangladesh Nationalist Party. ^[30] Amnesty International raised concerns about the fairness of his trial, citing irregularities in the proceedings. ^[31]

Following the fall of the Sheikh Hasina-led Awami League regime, Jamaat-e-Islami's ameer, Shafiqur Rahman, demanded the release of Islam and the restitution of the party's registration. ^{[32] [33]} Jamaat staged protests in Gazipur District demanding his release. ^[34] On 27 May 2025, he was acquitted by the Appellate Division of the Supreme Court. ^{[35] [36] [37]} On 28 May 2025, following a review of the case, he was released from jail. ^{[38] [39] [37]}