The summer of 1866 passed rather peacefully. There was a truce with Bokhara. Furthermore, although a treaty with Kokand was still two years off, Khudyar Khan of Kokand had accepted Russian peace terms after the fall of Khojend. In August, General Khryzanovsky appeared in Tashkent. Officially he was there to annex Tashkent, Kojend, and the territories in between to the Russian Empire. The Bokharan threat had forced Alexander II and Gorchakov to abandon plans for the creation of an "independent" state in the new territories. He was also there to take personal command of operations against Bokhara. He was dissatisfied with Romanovskii's handling of the truce talks with the Bokharans and, once again, jealous of his subordinate's successes.

Khyzanovsky immediately announced to the Emir via Romanovskii that he was waiting in Tashkent to conclude peace. To strengthen his chief's hand, Romanovskii threatened to renew hostilities unless a Bokharan envoy was dispatched to meet the governor-general. With no alternatives available, Muzaffar sent a negotiator. Talks broke down almost as soon as they started and Khryzanovsky issued an ultimatum on September 13.

After a week elapsed, Russian troops moved out of Khojend. Three days later when the ultimatum expired on September 23, Khryzanovsky had an army on the Bokharan frontier. Two days into October the fortress of Ura-Tyube was captured. On the l8th Djizak fell to the Russians. The occupation of that city ended the 1866 campaign season.

The Bokharan position was obviously weakening steadily. After the fall of Djizak, the semi-autonomous hakims of Shahr-i-Sabez deserted the Emir and declared their willingness to cooperate with a Russia advance on Bokhara. The following January an appeal by the Emir to the Viceroy of India for help was rejected. In the mean time, peace talks with the Russians had resumed once again but, as before, had failed.