After Germany's annexation of Austria in March 1938, Löhr joined the German Luftwaffe, and in 1939, he commanded its Fourth Luftflotte. During the invasion of Poland in September 1939, his aircraft destroyed Polish communications and traffic lines. In early April 1941, Löhr was assigned a similar task against Yugoslavia, with the additional charge of paving the way for advancing army units. On the morning of 6 April 1941, without a declaration of war, Löhr's bombers attacked Belgrade. They destroyed the Yugoslav command structure but also killed 1,500 civilians.
Promoted to colonel general on 9 May 1941, Löhr was supreme commander of the bloody German airborne assault of Crete, beginning on 20 May 1941. After the invasion of the Soviet Union on 22 June 1941, he commanded 4th Air Force Group in the southern part of the front. In July 1942, Adolf Hitler appointed him to command Twelfth Army in the Balkans (renamed Army Group E in January 1943). From 1943, Löhr additionally acted, with several interruptions, as supreme commander, Southeast. His task was to suppress the resistance movements and defend Greece against Allied landings.
In the summer of 1944, Soviet forces advanced toward Bulgaria and Hungary and threatened to cut off German units in the Balkans. Therefore, Hitler authorized a withdrawal through Yugoslavia to Hungary. Under constant partisan attacks, Löhr's army nonetheless slowed the Soviet advance until the end of the war. A prisoner of war of the Yugoslavian government from 11 May 1945, Löhr was tried for war crimes by a Yugoslav military court, sentenced to death, and executed in Belgrade on 26 February 1947.
Diakow, Jaromir. Generaloberst Alexander Löhr. Freiburg, Germany: Herder, 1964.; Hnilicka, Karl. Das Ende auf dem Balkan 1944/45: Die militärische Räumung Jugoslawiens durch die deutsche Wehrmacht. Frankfurt, Germany: Musterschmidt, 1970.; Orlow, Dietrich. The Nazis in the Balkans. A Case Study of Totalitarian Politics. Pittsburgh, PA: University of Pittsburgh Press, 1968.