Nowotny joined the Luftwaffe in 1939 and completed his fighter pilot training in 1941, after which he was posted to Jagdgeschwader 54 "Grünherz" (JG 54) on the Eastern Front. Nowotny was the first pilot to achieve 250 victories – 194 in 1943 alone – earning him the Knight's Cross of the Iron Cross with Oak Leaves, Swords and Diamonds on 19 October 1943. For propaganda reasons, he was ordered to cease operational flying.