It was initially used for daylight ground attack missions during the Battle of Moscow, but this proved to be costly since the aircraft was unarmored. Armor and additional guns were retrofitted to the existing aircraft to make it more effective, but the evacuation of the sole factory building the Pe-3 in October 1941 limited the number of aircraft available and many units of the Soviet Air Forces flying the Pe-3 were either disbanded or converted to other aircraft.
The Pe-3 was initially used for daylight ground attack missions during the Battle of Moscow but proved costly due to its lack of armor. Armor and additional guns were retrofitted to improve its effectiveness, though the evacuation of the sole factory building it in October 1941 limited the number of available aircraft, causing some units within the Soviet Air Forces flying the Pe-3 to be disbanded or converted to other types.