In Muharram ah 617/March 1220 ce Chinggis Khan led his armies to Bukhara as part of a larger campaign against the Khwārazmshāh Empire (616–621/1220–1225). The city quickly surrendered and was rapidly integrated into the growing Mongol Empire. In the subsequent decades, Bukhara enjoyed a speedy recovery under the stewardship of a series of Mongol officials, who patronized religious institutions, repaired the damage caused by the invasion, and mitigated some of the excesses of the Mongol armies stationed in Transoxania. Yet this revival was stunted in the second half of the 13th century when the Mongol Empire was divided by war. During this period different factions contested control of Transoxania, and Bukhara became the target of periodic raids and attacks. A full rehabilitation of the city had to wait until after 716/1317–1318, when alliances between the Mongol military elites and the popular religious leaders of Bukhara facilitated a new period of stability that would last until the fall of the last effective khan, Qazān Sultan, in 746/1346. Bukhara’s status as an intellectual, economic, and political capital of Transoxania was diminished during the period of Mongol rule. Samarqand was designated as the administrative capital of Transoxania for much of this period, and the presence of Mongol forces in Nakhshab saw Bukhara subordinated to the itinerate court of the Chaghadaid-Mongol princes. Nevertheless, the city continued to be seen as an important center of religious scholarship, and its prestige was boosted by the fact that it served as the base for two of the leading Sufi movements of its time, the Kubrawiyya and the Naqshbandiyya.
In the 19th century, the Emirate of Bukhara was one of three independent Uzbek principalities known as khanates. Ruled by the Manghit amīrs, Bukhara was the biggest and most important of the southern Central Asian polities and one of the major power centers in the wider region. To the readers of 19th-century European travelogues, Bukhara was known for the despotism of its rulers notorious for their cruelty and strange tastes. From a geopolitical point of view, the Bukharan Emirate was part of an anarchic transition space between Central and South Asia made up of half a dozen petty principalities without centralized power structures. While the bulk of the 19th- and 20th-century secondary sources stress the despotism of its amīrs and its isolation in view of the declining caravan trade on the Central Asian caravan routes, Bukhara and other urban centers such as Samarqand and Qarshi were embedded in transregional religious and trading networks. As a crossroads of commerce and an important religious center, Bukhara in particular and other Transoxanian towns as well attracted flows of goods and people from all directions and was well connected to other places and areas such as Siberia, China, India, and Persia. In the second half of the 19th century, the Emirate of Bukhara and its neighbors north of the Āmū Daryā River came into the focus of Russia. After a series of military defeats in 1868, Bukhara was turned into a Russian protectorate, which finally became a People’s Republic after the Bolshevik conquest in 1920. This political entity was absorbed into the emerging Soviet Union in 1924.