Stupnagal remained in the army and in October, 1941, was given command of the 17th Army. He took part in Operation Barbarossa but was taken ill in October, 1941.
As part of the July Plot Stupnagal gave the orders for the arrest of over 1,200 Gestapo and Schutz Staffeinel (SS) in France. When he heard the plot had failed he tried to commit suicide by shooting himself in the head. Although blinded Stupnagal recovered to face trial for treason. Karl Stupnagal was found guilty and was executed at Ploetzwnsee Prison on 30th August, 1944.