In 1363, Tughlugh Timur, who had recently taken control of Transoxiana and had executed many of its local leaders, appointed Ilyas Khoja as its ruler.
Together they faced an army of Moghuls and local tribes loyal to Ilyas Khoja, and defeated them at the battle of Stone Bridge [ru].
Shortly afterwards, Tughlugh Timur died and Ilyas Khoja left for Moghulistan to take power.
In May, he defeated Amir Husayn and Timur at the battle of Tashkent, but when he arrived before the gates of Samarkand its inhabitants refused to let him enter, and the subsequent siege was disastrous.
The Dughlat amir Qamar ud-Din then usurped the khanship; he was probably responsible for Ilyas Khoja's death.