Gur Emir underground crypt contains graves of three more governors except for Amir Temur and Muhammad Sultan. They are Temur's sons Miranshah (1366-1408) and Shahruh (1377-1447), and his grandson Mirzo Ulugbeg (1396-1449). Miranshah was Temur's third son and in the age of 14 was appointed by his father, the governor of Khurasan, with Heart as the center. In the 1390s Miransnah receives "the throne of Hulagu", i.e. becomes the governor of the the western territories of Temur's empire. In 1408 Miranshah was killed in a battle with Turkmens. Several years later his remains were brought in Maverannahr and buried in Gur Emir.

Amir Temur's youngest son, Shahruh was enthroned in Khurasan and after father's death he became the supreme governor of the empire. He gave Maverannahr to his son Mirzo Ulugbeg who reigned there over forty years being supported by his father's power. Shahruh died during a military campaign and was buried in Herat. Ulugbeg twice compained in Khurasan and finally took Hearts throne. Then Shahruh's remains were reburied in Samarkand. In1449 Ulugbeg's son Abdullatif rose against his father, dethroned him and killed. Abdullatif was soon dethroned, and remains of Ulugbeg were buried in Gur-Emir.