He was abducted by the Al-Badr militia as part of a plan to kill the renowned intellectuals of the country and was found dead on 18 December 1971 at Rayer Bazaar in Dhaka.
His wife, Shyamoli Nasrin Chowdhury is a national award-winning educationist and former principal of Udayan School.
As part of a planned assault on Bengali intellectuals, Chowdhury was abducted by Al-Badr militants on 15 December 1971.
Moulana Abdul Mannan, one of the key collaborators of the Pakistan army during the Liberation war of Bangladesh, was directly involved in the abduction and killing of Chowdhury.
In the mid of July, Moulana Mannan, an organizer of Al-Badr, came to Chowdhury for a shelter as he was shelterless and destitute at that time.
[citation needed] On 18 December, Chowdhury was found dead along with other intellectuals at Rayer Bazar mass grave.
[citation needed] On 3 November 2013, Chowdhury Mueen-Uddin, a Muslim leader based in London, and Ashrafuz Zaman Khan, based in the US, were sentenced in absentia after the court found that they were involved in the abduction and murders of 18 people – nine Dhaka University teachers, six journalists and three physicians including Chowdhury – in December 1971.