At the high point of the Russian conquest of Turkestan, in 1867, he became Governor-General of the new province of Turkestan, and held the post until his death, making himself a name in the expansion of the empire in Central Asia. The western part of the Khanate of Kokand along the Syr Darya had already been captured, and the independence of the rest of that country became merely nominal. He accomplished a successful campaign in 1868 against the Emirate of Bukhara, capturing Samarkand and gradually subjugating the whole country. accompanied Kaufmann in his campaigns. During the Khivan campaign of 1873, he attacked Khanate of Khiva, took the capital, and forced the Khan to become a vassal of Russia. This was followed in 1875 by the campaign against Kokand, in which Kaufman defeated the uprising khan, Nasreddin, after an anti-Russian uprising against the previous ruler, Khudoyar. The fiction of Kokand's independence was ended, and the remaining rump of the Khanate in the Ferghana Valley was annexed. This rapid absorption of these Khanates brought Russia into proximity to Afghanistan, and the reception of Kaufmann's emissaries by the Sher Ali Khan was a main cause of the Second Anglo-Afghan War.
Administration
The various temporary statutes under which Turkestan was administered from 1867-1886 gave von Kaufmann a great deal of latitude in policy. In 1868 he contacted experts in Moscow to identify Alexie to create an expedition to document the countries natural history. Whilst Kaufmann was still extending the borders of the Russian Empire, he was creating a team to investigate and document the new territory. Kaufmann's team included statisticians, the Fedchenkos, the war artistVasily Vereshchagin and later the educationalist Nikolai Ostroumov. Kaufman wanted an investigation of a "newly and scarcely explored region". Kaufmann set up a Tashkent outpost of the Moscow Society of Devotees of Natural Science, Anthropology, and Ethnography. The Fenchenkos made three separate explorations between 1868 and 1872. These investigations were central to the Governor-General's policy as he wanted to see this information shared with Russians as well as locals The local newspaper was used to publish the scientific findings. Kaufmann targeted the 1872 Moscow All-Russian Technical Exhibition as an opportunity to display the research of this new part of the Russian empire. Kaufmann was allowed to carry out administrative negotiations with neighbouring states on his own account, to establish and oversee the expenditure of the budget, set taxes, and establish the privileges of Russian subjects in the General-Gubernatorstvo; he also had the power to confirm and revoke death sentences passed in the Russian military courts. Nowhere else in the Russian Empire did a Military Governor-General have this kind of independence from central control, and nowhere else was there such obvious pessimism about the region’s potential for integration into the main body of the Empire. Isolated geographically from European Russia by an expanse of Steppe that took two months to cross, it was isolated still more decisively in the minds of Tsarist officials by its dense, ancient and settled Islamic culture. In its early years under Kaufmann, Turkestan was thus also administratively isolated, with many distinctive institutions within the military bureaucracy, that was loosely superimposed on a largely unreformed native administration. Although Kaufmann was unable to induce his government to support all his ambitious schemes of further conquest, he was still in office when General Mikhail Skobelev, the hero of the Russo-Turkish war of 1877, was despatched from Tiflis in 1880 and 1881 against the Turkomans of the Akhal-Teke Oasis. Skobelev, although being the effective military governor of the Fergana valley, directing matters from Margelan and New Margelan, was cut short in this second campaign of his in the area. He was recalled.. General Chernyayev, the conqueror of Tashkent in 1865, was appointed as his successor. There are various species of plants are named after him including Eremurus kaufmannii, Eremostachys kaufmanniana, Tulipa kaufmanniana, Gentiana kaufmanniana, and Statice kaufmanniana.