The shah of Khwarezm had fled after the Battle of Khojend, and the Mongols have pursued him to a Khwarizmian defensive line established near Bukhara in the region of present central Uzbekistan.
Arranging ten Mongol cavalry divisions into four columns, Genghis Khan has three of them converge to collapse the shah’s right (southern) flank near the city of Samarkand, while he personally leads the forty-thousand-man fourth column against the rear flank, approaching Bukhara from the west.
The shah abandons Bukhara to concentrate on the larger force, enabling the Mongols, after a brief siege, to capture and sack the city.
According to Juvaini, when Genghis Khan conquered Bukhara "he contented himself with looting and slaughter only once and did not go to the extreme of a general massacre" as he did in Khorasan, although most of the city accidentally burns.
He chooses a moderate path between mercy and punishment because the population readily submits while the garrison in the citadel resists.
Although he spares most adults, Genghis Khan kills thirty thousand Kankali Turks who are "taller than the butt of a whip" on account of their loyalty to Sultan Muhammud, then conscripts all remaining able-bodied men into service.