In August 1941, soon after the German invasion, Shtemenko was appointed as Sharokhin's deputy, an office he held until after the Battle of Moscow, when he was assigned as chief of the Near East department. As such, Shtemenko monitored the conditions of the Soviet troops stationed in the recently occupied Iran. In June 1942, he replaced Sharokhin as the department chief. Shtemenko took part in the operational planning of the Battles for Crimea, the Caucasus and Stalingrad. In May 1943, he was promoted to be the chief of the Operations Directorate, serving directly under Marshal Alexander Vasilevsky. In November of that year he escorted Stalin to the Tehran Conference.