Baydukov served as deputy commander of the 31st Mixed Aviation Division from December 1941. In February, he became commander of the division. In March 1942, he became commander of the Air Force of the 4th Shock Army. In May 1942, Baydukov was appointed commander of the 211th Mixed Aviation Division. In June 1942, he became commander of the 212th Assault Aviation Division. In May 1943, the division became the 4th Guards Assault Aviation Division. In January 1944, Baydukov became commander of the 4th Assault Aviation Corps.