In the summer of 1865 the amir of Bukhara, Muzaffar ad-Din, demanded that the Russians withdraw from Tashkent; in response, all Bukharan merchants on Russian territory were arrested and their goods sequestered. In early 1866 Cherniaev crossed the Amu-Darya, but failed to capture the Bukharan town of Jizak, after which he was recalled and replaced by General Romanovskiy. In May 1866, in the locality of Irjar, the Bukharan army under the command of the amir himself was defeated and fled. The battle was followed by the capture of Khojend (which was a part of the Khanate of Qoqand); it was officially annexed to Russia together with Tashkent, and the Khanate of Qoqand was thus reduced to the Ferghana valley.
The conditions for peace that the Russians submitted to Bukhara were deliberately made unacceptable, and when they were rejected, Russian troops resumed the offensive and took Ura-Tübe and Jizak. In July 1867 the Russian government again reorganized the conquered territories, creating the Governorate-General of Turkestan with its center in Tashkent, comprising all lands conquered by Russia in Central Asia since 1847.
A year later, an administrative reform of the steppe regions was carried out (cf. map 44), which, together with the transfer of the Russian customs border from the old Orenburg-Irtïsh line that had taken place in 1865, marked the final annexation of the Qazaq steppe. Romanovskiy was replaced by the first GovernorGeneral of Turkestan, General A.P. von Kaufman, who was given almost unlimited authority.

In January 1868 Kaufman imposed a commercial convention on Qoqand, which guaranteed various privileges for the Russian merchants and symbolized the end of hostilities between the khanate and Russia (no formal peace treaty was concluded). In April 1868, Amir Muzaffar ad-Din, yielding to militant mullas of Bukhara and Samarqand, proclaimed a holy war against Russia. On May 1 Kaufman defeated the Bukharan troops on the ChopanAta heights near Samarqand, and the next day Samarqand fell. On June 2 the army of Bukhara under the amir was again routed at Zirabulaq heights, near Katta-Qurghan, after which the amir capitulated, and on June 30 he signed the peace conditions submitted by Kaufman. The khanate recognized the loss of all the territories captured by the Russians, agreed to pay a war indemnity, and opened the country to Russian merchants.
The fall of Samarqand and the capitulation of the amir provoked a rebellion by the amir’s son #Abd al-Malik, supported by the semi-independent tribal chieftains (beks) in Shahrisabz. The rebellion was suppressed the same year by Russian troops, who later conducted an expedition to the upper course of the Zerafshan, which resulted in the Russian annexation of several small mountain principalities in that region.