Under al-Musta'in (), he was given command of the summer expedition ("sa'ifah") of 863 and undertook a successful raid against the Byzantines, but when he gave the governor of Malatyah, 'Umar al-Aqta', permission to continue with the invasion on his own, the Byzantines struck back and killed 'Umar at the disastrous Battle of Lalakaon. Following the flight of al-Musta'in to Baghdad in 865, Ja'far was one of the few officers who remained behind in Samarra, and instead supported the rival caliph al-Mu'tazz (). He is last mentioned that year, when al-Mu'tazz placed him in charge of his guard ("haras"). Ja'far's son Mansur ibn Ja'far al-Khayyat later rose to some prominence, likewise serving as a military commander and governor until he was killed in battle during the Zanj Rebellion in 872.