On 1 September 1933, Stumpff, with the rank of lieutenant colonel, became head of personnel in the (illegal) Luftwaffe.

After the Luftwaffe became formally legal in Germany because of the Nazis rejection of the terms of the Treaty of Versailles, Stumpff served as its chief of staff from 1 June 1937 until 1 January 1939, when he was succeeded by Hans Jeschonnek In 1938, Stumpff was promoted to the rank of General der Flieger.

Until the end of 1943 Stumpff commanded Luftflotte 5, with which he took part in the Battle of Britain, operating out of Norway against Scotland and Northern England.

In January 1944, Stumpff commanded Luftwaffe forces in the Defense of the Reich campaign against the Allied bombing attacks.

On 8 May 1945, Stumpff served as the Luftwaffe representative at the signing of the unconditional surrender of Germany in Berlin.