The Mongols had laid siege to the border town of Otrar, but finding its defences obdurate, a large force commanded by Genghis and his youngest son Tolui detached from the vanguard and set off southwards, towards Transoxiana.

Although the city was then comprehensively looted and pillaged, it revived slowly under the Pax Mongolica, and then, in the late 14th-century, returned to worldwide prominence as the capital of the Timurid Empire.

[1]: 113  The Shah, who distrusted his commanders and had not yet implemented his desired methods of administration, decided on a strategy of distributing troops inside his major cities, such as Samarkand, Balkh and Otrar.

[5]: 78  The city was stunned by the Mongol approach, which had been through an area previously thought impassable, and, after a sortie was annihilated along the Amu Darya, the lower town surrendered and was promptly pillaged.

He rebuilt the palaces and the city walls, which were still in ruins, and commissioned numerous mosques, gardens and pavilions to re-establish Samarkand's importance on an international level.