After the death of Abu Said in 1469 (see map 22) and a brief succession fight in Khorasan, Heart was captured by Sultan Husain Baqarah, a greatgreat-grandson of Timur through #Umar Sheikh. At that time Khorasan was threatened by the Aq-Qoyunlu, who had replaced the Qara-Qoyunlu in western Iran just before the ill-fated campaign of Abu Said.
The Aq-Qoyunlu ruler Uzyn Hasan supported a Timurid contender, Yadira Muhammad (great-grandson of Shahrukh), who briefly occupied Heart in 1470, but Husain retook the city a month later, Yadira Muhammad was executed, and the next year the Aq-Qoyunlu troops withdrew from Khorasan. After this, for 25 years, the political situation in the Timurid realm was relatively stable. The regions north of the Amu-Darya were divided among the three sons of Abu Said, of whom Sultan Ahmad, the eldest, ruled Mavarannahr, Sultan Mahmud ruled Hisar, Chaghaniyan and Badakhshan, and #Umar Sheykh ruled Ferghana.
The rule of Sultan Husain Baqarah in Khorasan was a period marked by great cultural achievements. The court of Sultan Husain in Heart, which continued the traditions of Shahrukh’s court, became especially famous as a gathering place of artists and poets, the most prominent among whom were the Persian poet (and the head of the Naqshbandi Sufis of Khorasan) Jami, the Chagatai poet Navami (a friend and confidant of Sultan Husain), and the painter Behzad. As distinct from Sultan Husain, Sultan Ahmad was heavily under the influence of the Naqshbandi sheikh Khoja Harar, and the cultural life of Samarqand lacked the refinement of Heart. Thanks to the works of Navami, the Chagatai language (Also known simply as Turki), which emerged in the early 15th century, became fully developed as the literary language of the Central Asian Turks. With the cessation of the wars of conquest, the Chaghatay tribes apparently became more or less sedentarized by the end of the Timurid period.

The relative stability of the Timurid realm ended in the mid-1490s. Sultan Ahmad died in 1494; his younger brother, Sultan Mahmud, replaced him in Samarqand, but died several months later; #Umar Sheikh also died in 1495. Sultan Mahmud was succeeded by his son, Sultan Ali, who was an incompetent ruler. After the departure of Sultan Mahmud to Samarqand, he was succeeded in Hisar by his Amir Khusrawshah, who banished two sons of Sultan Mahmud and ruled this large appanage as an independent ruler. In Khorasan, Sultan Husain's son Badi az-Zaman, governor of Balkh, rebelled in 1497 and threatened Heart in 1498; Khusrawshah recognized his authority.
Two other sons of Sultan Husain rebelled in Merv and Abiverd, and Sultan Husain had to deal with these feuds, even as the Uzbeks were already beginning their invasion of Mavarannahr.