After the capture of Kazan, Russian troops did not completely control the territory of the former Khanate. Attacks on Russian messengers, merchants and service people continued, and tax collectors were killed. Punitive expeditions sent from Sviyazhsk and Kazan were not always successful. At the end of 1552, a real rebellion broke out. The rebels defeated several small Russian troops. On March 10, 1553, a detachment of governor Boris Saltykov, 400 dead archers and 500 Cossacks was defeated. The governor himself was captured and killed. The mass executions of the rebels could not stop the rebel movement. The center of the uprising was the city of Chalym . The rebels even restored the khan's power: one of the Nogai princes Ali-Akram, who arrived with a detachment of 300 Nogai, was invited to the throne. In 1553, forces were directed against the rebels under the command of Daniil Adashev, as well as the troops of Prince Mikulinsky , who operated along the Kama River. By the end of the year, the uprising was almost stopped.
In 1554, an uprising broke out with renewed vigor. The commander of the Russian forces was Prince Mstislavsky . The suppression of the uprising was accompanied by the cruel executions of its participants, and towers and fortresses were also built. In 1556, the center of the uprising, the city of Chalym , was taken. After that, further resistance was stopped. Some local peoples, weary of the endless war, began to oppose the Kazan Tatars. The khan was killed by the rebels themselves, and the main leaders of the movement died.
Strong economic decline, a sharp decline in population. A stone fortress was erected in Kazan, the Tatars were evicted from the city, and mosques were destroyed. After the uprising was suppressed, many lands of local feudal lords were confiscated and passed into the hands of the state, boyars, noblemen, clergy and those Tatars who recognized the new government. An increase in the Russian population in the territory of the former Khanate.