While still serving his sentence in the Gulag, Safarov was sentenced to death by a decree of a Special Collegium of the NKVD on 16 July 1942 following the German Invasion of the Soviet Union, ironically on the same day Safarov had signed the death warrant for the Romanovs 24 years prior. He was executed on 27 July 1942 in Saratov and was consigned to an unmarked grave.