On July 5, a few weeks following Germany's invasion of the Soviet Union, Babadzhanian was dispatched to Smolensk, where he assumed command of the 395th Rifle Regiment, 127th Rifle Division. His unit was involved in a rearguard action during a temporary retreat, putting up stiff resistance against Axis forces before turning once again to the offensive. His unit was the first to re-enter the city of Yelnya on September 8, 1941, an accomplishment that earned it a period of respite from the fighting. After a short rest and refit in Kursk, fighting soon enveloped that part of RSFSR and Babadzhanian's regiment engaged Axis forces in Fatezh and assisted in the evacuation of Kursk.