At the time of the German invasion of the Soviet Union in June 1941, Shestakov was serving with 69th Fighter Aviation Regiment on the Odessa front, and became the Regiment Leader on 16 July 1941. During the battle for Odessa 69th Fighter Aviation Regiment pilots achieved 94 air victories. The losses inflicted on the Romanian Air Force above Odessa in 1941 by Shestakov's fighter pilots compelled the Romanian High Command to withdraw its entire air force from the Eastern Front.