The Beginning of the Conquest of the Bukhara Emirate
After the capture of Tashkent, the Tsarist government’s next plan was to conquer the khanates one by one. All military operations were organized and directed from Tashkent. To achieve this, a policy aimed at preventing the khanates from uniting was pursued. In other words, the colonizers adhered to their fundamental principle: “Divide and rule.”
The Tsarist government recalled M. Chernyaev from Central Asia to St. Petersburg and appointed F. Romanovsky as the governor of the Turkestan region in his place. In 1866, using the pretext that the Bukhara Emirate was preparing for war against Russia, F. Romanovsky requested permission from the Emperor to launch a military campaign against it.
Once this proposal was accepted by the government, Romanovsky began occupying the middle reaches of the Syr Darya. The first battle occurred on May 8, 1866, near the village of Irjar, where the Emir’s forces were defeated due to military inferiority. F. Romanovsky then halted the pursuit of the Bukhara army and advanced toward Khojand, a strategic location linking Tashkent, Kokand, Balkh, and Bukhara, before confronting the Bukhara Emirate and the Kokand Khanate.
In May, Khojand Fortress was besieged by the troops of the Governor-General of Turkestan and bombarded with 20 cannons. The siege continued until the next morning, followed by an assault. After repeated attacks, the city was shelled again. The siege and bombardment lasted two days. The city defenders fought bravely for every inch of territory, but the colonizers’ forces, superior in both military equipment and numbers, broke through the defenses by the night of May 24. The streets were left strewn with the bodies of defenders and civilians, and buildings lay in ruins.
Establishment of Russian Imperial Protectorate over the Bukhara Emirate
Governor-General von Kaufman decided to continue the conquest of Central Asia by seizing the Bukhara Emirate. The Emirate’s military was weakened due to continuous wars with the Kokand Khanate, internal disputes, and technological inferiority. Von Kaufman studied the border territories carefully and proposed a new treaty to Emir Muzaffar, which would alter the border in Russia’s favor. The Emir refused to sign.
Blaming Emir Muzaffar for not preparing to accept the General-Governor’s authority, von Kaufman assembled a military detachment of over 4,000 troops and began the capture of Samarkand in April 1868. However, his assumption that Emir Muzaffar’s forces were concentrated in Samarkand was incorrect.
At this time, Bukhara forces were stationed on the Choponota hill. On May 1, 1868, von Kaufman attacked the hill. Despite continuous fire from rifles and cannons, the Russian troops crossed the river and took the hill, forcing the Emir’s advanced units to retreat. The second battle took place at Zirabuloq Hill. Despite resistance, the Emir’s forces were again defeated, and the Tsarist troops entered Samarkand without a fight. Von Kaufman sent a letter to Emir Muzaffar proposing peace on terms favorable to Russia, including covering military expenses and recognizing Russian possession of all territories seized since 1865, but received no reply.
Local populations also resisted Russian military campaigns. For example, during Kaufman’s campaigns against Bukhara, the residents of Urgut fought Tsarist forces. When General Abramov was sent to demand the city’s surrender, the locals refused. Fierce fighting ensued, and despite artillery superiority, the fortress was eventually taken by the colonizers. Following Urgut, Russian forces captured the city of Kattaqorgon.
In Samarkand, local resistance was led by the rulers of Kitob (Jorabek) and Shahrisabz (Bobobek). On June 2, 1868, they, along with insurgents from Samarkand, attacked the Russian garrison. Reinforcements arrived on June 6, and after four days of intense fighting (June 4–7), the defenders suffered heavy losses. By June 8, Russian forces reached the fortress, forcing the defenders to retreat to the mountains.
Bukhara Emirate as a Russian Protectorate
The Tsarist government established the Zarafshan District, comprising the Samarkand and Kattaqorgon regions, under the administration of General Abramov. After the battle of Zirabuloq, Emir Muzaffar accepted his defeat and agreed to the new territorial terms proposed by von Kaufman, marking the end of the second phase of Russian imperial conquest.
On June 23, 1868, in Samarkand, Emir Muzaffar signed a treaty making the Bukhara Emirate a Russian protectorate. The treaty acknowledged that the Emir had caused the war and required 500,000 rubles to cover Russian military expenses as a symbol of eternal friendship. Territories from Tashkent to Samarkand, including Khojand, Uratapa, Panjikent, Jizzakh, Samarkand, and Kattaqorgon, came under Russian control. The Emir retained authority over his remaining territories but had to follow the directives of the Turkestan Governor-General. For this political dependence, historians often describe the Bukhara ruler as a vassal. Russian merchants were allowed to trade freely and were protected; customs duties could not exceed 2.5% of the goods’ total value, and they were permitted to move goods freely to other countries.
This treaty, humiliating and impoverishing the Emirate, sparked opposition. Emir Muzaffar’s eldest son, Abdumalik To’ra, along with Jorabek and Bobobek, continued the fight to liberate Samarkand. They declared Abdumalik To’ra as Emir and captured Shahrisabz, then Qarshi and Karmana. However, lacking modern weapons, their forces were gradually pushed back by troops under General Abramov. Abdumalik To’ra fled to the Khiva Khanate and later to Afghanistan, eventually reaching Peshawar, where he died in 1909.
Thus, the second phase of Russian conquest in Central Asia ended with the capture of Samarkand and the establishment of the Bukhara Emirate as a Russian protectorate. In 1873, a new treaty gave Russia the right to appoint a representative in the Emirate, effectively controlling all internal and external political matters. Article 14 stipulated: “No person shall be received by the Bukhara government without permission from the Russian government.” The representative would deliver instructions to the Emir daily, who would formally approve them. P. Lessar became the first Russian representative in Bukhara.
The representative, effectively Bukhara’s unofficial governor, headquartered in Kogon, 15 km from Bukhara. This allowed the Tsarist government to control the Emirate through the Emir and his officials without fully incorporating it into the empire. Between 1869–1870, the Russian Foreign Ministry negotiated with Britain to define borders in Afghanistan and Central Asia, resulting in the delimitation of the Amu Darya border along the Panj region. The border between Bukhara and Persia was set on December 10, 1881, through a secret treaty signed by the Russian ambassador in Tehran and the Shah of Persia. Later negotiations (1885–1887) by an Anglo-Russian commission finalized the border between the Bukhara Emirate and Afghanistan.
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Russian Empire 
Nasrullah Khan 