Following the death of Chinggis Khan in 1227, his empire was divided among his three sons. Despite the potential for serious fragmentation, Mongol law maintained orderly succession for several more generations, and control of most of Mawarannahr stayed in the hands of direct descendants of Chaghatai, the second son of Chinggis. Orderly succession, prosperity, and internal peace prevailed in the Chaghatai lands, and the Mongol Empire as a whole remained strong and united.

In the early fourteenth century, however, as the empire began to break up into its constituent parts, the Chaghatai territory also was disrupted as the princes of various tribal groups competed for influence. One tribal chieftain, Timur (Tamerlane), emerged from these struggles in the 1380s as the dominant force in Mawarannahr. Although he was not a descendant of Chinggis, Timur became the de facto ruler of Mawarannahr and proceeded to conquer all of western Central Asia, Iran, Asia Minor, and the southern steppe region north of the Aral Sea. He also invaded Russia before dying during an invasion of China in 1405.

Timur initiated the last flowering of Mawarannahr by gathering in his capital, Samarqand, numerous artisans and scholars from the lands he had conquered. By supporting such people, Timur imbued his empire with a very rich culture. During Timur's reign and the reigns of his immediate descendants, a wide range of religious and palatial construction projects were undertaken in Samarqand and other population centers. Timur also patronized scientists and artists; his grandson Ulugh Beg was one of the world's first great astronomers. It was during the Timurid dynasty that Turkish, in the form of the Chaghatai dialect, became a literary language in its own right in Mawarannahr--although the Timurids also patronized writing in Persian. Until then only Persian had been used in the region. The greatest Chaghataid writer, Ali Shir Nava'i, was active in the city of Herat, now in northwestern Afghanistan, in the second half of the fifteenth century.

The Timurid state quickly broke into two halves after the death of Timur. The chronic internal fighting of the Timurids attracted the attention of the Uzbek nomadic tribes living to the north of the Aral Sea. In 1501 the Uzbeks began a wholesale invasion of Mawarannahr.