From 1937 to 1939, he served as commander-in-chief of the Soviet Air Force. In July 1940, after the Soviet occupation of the Baltic States, Loktionov was appointed commander of the Special Baltic Military District. In June 1941 he was arrested on fabricated charges of participation in an anti-Soviet conspiracy. Under interrogation, he was brutally beaten by infamous NKVD interrogators Boris Rodos and Lev Shvartsman, and lost consciousness several times from the torture. He was later put in a "confrontation" with Kirill Meretskov; the NKVD used Loktionov's bloodied appearance to intimidate Meretskov. After the German Invasion of the Soviet Union, he was moved from a local NKVD prison to the Kuybyshev prison, where he was shot without trial on 28 October along with many others on personal orders of Beria. He was posthumously rehabilitated in 1955.