The middle of the 19th century became the starting point for the Russian Empire in terms of the conquest of the Kokand Khanate and the Bukhara Emirate, as well as its final positions consolidation in the region by creating the Turkestan Governor-General in the annexed territories in 1867. The defeat of the Russian Empire in the Crimean War forced the government to take more decisive measures to annex Kokand and Bukhara through a large-scale military campaign, however the need to solidify its hold on the region as soon as possible required the command to make some new strategic decisions and cooperate with representatives of the local elite, merchants and clergy. The article is intended to significantly fill the historiographical gap in the research of the cooperation between the Russian command and the Muslim institutions within the framework of the annexation of Central Asia by introducing and analyzing previously unpublished sources from the State Archive of the Orenburg Region. The article reviews examples of cooperation with representatives of the elite, merchants and clergy, their influence on the possible peaceful settlement of the conflict or its escalation, including the issue of collaboration and espionage in the Muslim environment, possible potential benefits and the need for cooperation with the Russian army. The conclusions of the article allow revising traditional views on the positions of Islamic leaders, as well as reevaluating the significance of a religious factor as one of the most important elements in the system of confrontation of Asian khanates with Russia.