He was killed on Thursday the ninth of Jumada al-awwal, 786 A.H. (ca. 1385) during the reign of Sultan Barquq. His death was in accordance with the fatwa of a jurist from the Maliki madhab, which was endorsed by a jurisprudent of the Shaf'i madhab. Accusations against him included rafd, defamation of senior Islamic personages, the companions and family of Muhammad, Aisha, Abu Bakr and Umar, following the Nusayri faith, and permitting the drinking of wine.[4]
These accusations were first brought against him by two of his former students from Jabal Amil, who were also former Twelver Shiites. One of them, Yusuf ibn Yahya, submitted a report (which included the signatures of 70 former Shiites from Jabal Amil) to the authorities detailing al-Amili's "vile doctrines and abominable beliefs."[5][6]
However, according to Shia biographer al-Khwansari, al-Amili denied these charges in a letter to the governor of Damascus, protesting his love for "the Prophet and all who loved him, all the Companions without exception."[7] He was imprisoned for one year, then beheaded by sword. His corpse was then crucified and stoned in Damascus whereby it was burned and the ashes were discarded into the air.