While the Shah planned to defend his major cities individually, the Mongols laid siege to the border town of Otrar, and struck further into Khwarazmia.

A Mongol force, estimated to number between 30,000 and 50,000 men and commanded by Genghis himself, traversed the Kyzylkum Desert, previously considered impassable for large armies.

Although Bukhara was then destroyed by fire, the destruction was relatively mild compared to elsewhere; within a short space of time the city was once again a centre of trade and learning, and it profited greatly from the Pax Mongolica.

The city was guarded by the Ark of Bukhara, a fortress established in the fifth century which served as a citadel; the farmlands were extensively irrigated using water from the River Zeravshan.

[7] The Khwarazmian dynasty had usurped the Qara-Khitai, already destabilized by refugees fleeing the conquests of Genghis Khan, who had begun to establish hegemony over the Mongol tribes.

Outraged, Genghis left his ongoing war against the Chinese Jin dynasty, and rode westwards in 1219 with most of his army, leaving only a minimal force behind under the command of Muqali.

[17] The Mongol armies arrived in Khwarazmia in waves: first, a vanguard led by Genghis' eldest son Jochi and the general Jebe crossed the Tien Shan passes, and started laying waste to the towns of the eastern Fergana Valley.

[18] Genghis soon arrived with his youngest son Tolui, and split the invasion force into four divisions: while Chagatai and Ogedai were to remain besieging Otrar, Jochi was to head northwest in the direction of Gurganj.

[21] The Shah distrusted most of his commanders, the only exception being his eldest son and heir Jalal al-Din, whose military skill had been critical at the Irghiz River skirmish the previous year.

[25] Deducing the Shah's strategy, Genghis bypassed the stronghold of Samarkand and traversed 300 miles of the Kyzylkum Desert to reach Bukhara on 7 February 1220.

As contemporaries thought the Kyzylkum impassable by large armies, modern historians such as H. Desmond Martin and Timothy May have considered the manoeuvre a tactical masterstroke.

[25] Juvaini records that the garrison at Bukhara was commanded by a man named Gür-Khan;[29] the early 20th century historian Vasily Bartold suggested that this may have been Jamukha, an old friend-turned-enemy of Genghis.

[25][31] The major military action of the siege came on the second or third day, when the Sultan's troops, numbering between 2,000 and 20,000, sallied forth; Juvaini records that they were annihilated by the Mongols on the banks of the river: When these forces reached the banks of the Oxus, the patrols and advance parties of the Mongol army fell upon them and left no trace ... On the following day from the reflection of the sun the plain seemed to be a tray filled with blood.The historian Paul Buell notes that the sortie, conducted solely by the Sultan's auxiliary troops and not by the city garrison, may have just been an attempt to flee; he attributes their willingness to leave to the fact that Bukhara was a very recent Khwarazmian conquest, having been taken from the Qarakhanids less than a decade previously.

[42] Shah Muhammad died destitute on an island in the Caspian Sea, and the Mongols systematically besieged and took every major city in his empire;[43] his son Jalal al-Din would put up the most resistance but was eventually defeated at the Battle of the Indus in November 1221.