He briefly served as Minister of the MGB in 1946, but was soon replaced by his rival Viktor Abakumov. Merkulov later served as Minister of State Control, replacing Lev Mekhlis. Following Stalin's death, he was arrested and executed by firing squad along with his patron Beria and five other associates on 23 December 1953. It is rumored that all six bodies were cremated and buried in an unknown location near Moscow.