He also served for a brief time as head of State Police and as an SD Chief in the East Prussian-town of Tilsit (now Sovetsk, Russia), and was replaced in both positions by fellow Gestapo member Dr. Heinz Gräfe in October and November 1937.
On 6 April 1945, he prosecuted Hans von Dohnanyi in Sachsenhausen concentration camp while the defendant lay semi-conscious on a stretcher having contracted a serious infection and the proceedings ended with him being condemned to death by Sturmbannführer Otto Thorbeck.
Among the condemned were Lutheran clergyman Dietrich Bonhoeffer, General Hans Oster, Army Chief Judge Dr. Karl Sack, Captain Ludwig Gehre and former head of the Abwehr Admiral Wilhelm Canaris.
[3] The court's prosecution employed torture methods such as thumb screwing and mechanical stretching devices on the accused, who were subsequently sentenced to death after a brief trial and executed by hanging on 9 April 1945, only around two weeks before the camp's liberation.
The Army's counterintelligence division took a particular interest in Huppenkothen's knowledge of Communism and his work as a Gestapo official in searching for members of the Communist resistance and espionage group, the Red Orchestra.