The Khanate reached its greatest extent and influence under its penultimate Abu'l-Khayrid ruler, the scholarly Abdullah Khan II (r. 1557–1598).

After his death in 1747, the khanate was controlled by the non-Genghisid descendants of the Uzbek emir Khudayar Bi, through the prime ministerial position of ataliq.

In 1785, his descendant, Shah Murad, formalized the family's dynastic rule (Manghit dynasty), and the khanate became the Emirate of Bukhara.

[8] However, the Uzbek tribes remained nomadic, living a life on the steppe, and Abu'l Khayr Khan had no interest in conquering the lands of Transoxiana or Khorasan.

In the 1490s Muhammad Shibani swept through Central Asia and conquered Samarqand, Bukhara, Tashkent, and Andijan from 1500 to 1503.

[8] A turning point in the conflict between the two was the Battle of Sar-i Pul in the spring of 1501, which resulted in Babur's defeat.

[8] The ruler of Herat, Sultan Husayn Bayqara, attempted to launch a campaign to Transoxiana but it proved to be abortive.

Baqi Muhammad Khan, despite his short reign, carried out administrative, tax and military reforms in the country, which contributed to its further development.

The most famous Uzbek poet is Mashrab, writing in both Chagatai and Persian, who composed a number of poems in that are still popular today.

[15] In the sources of the second half of the 17th century, the expression "92 Uzbek tribes" is used in relation to the part of the population of the Bukhara Khanate.

In 1719–1720, after the flight of Ibrahim-bey from Bukhara, Khudayar-bey, who was in Balkh, was allowed to return to power, giving him the inheritance of Karshi, which was the result of the policy of his son Muhammad Hakim-bey.

During the campaign of the Afsharid ruler of Persia Nadir Shah to Maverannahr in 1740, Muhammad Hakim-biy went to peace negotiations with him, thus saving the country from war and strengthening his power.

Under Mohammad Rahim Bi, the Bukhara Khanate was able to expand to the regions of Hissar, Samarqand, Urgut, the Zarafshan Valley, Kulab, Jizzakh, and Ura Tepe.

The "Divan" of Muhammad Shibani's poems, written in the Central Asian Turkic literary language, is currently kept in the Topkapi manuscript collection in Istanbul.

The manuscript of his philosophical and religious work: "Bahr ul-Khudo", written in the Central Asian Turkic literary language in 1508, is located in London.

It was written in the Turkic-Chagatai language in 1507 shortly after his capture of Khorasan and is dedicated to his son, Muhammad Timur-Sultan (the manuscript is kept in Istanbul).

Ubaydullah Khan was a very educated person, he skillfully recited the Koran and provided it with comments in the Turkic language, was a gifted singer and musician.

The formation of the most significant court literary circle in Maverannahr in the first half of the 16th century is associated with the name of Ubaydullah Khan.

[23] In the Abu'l-Khayrid era in the Bukhara Khanate, Agha-i Buzurg or "Great Lady" was a famous scholarly woman-Sufi (she died in 1522–23), she was also called "Mastura Khatun".