At Hartheim, Stangl served under Christian Wirth as assistant supervisor in charge of security. When Wirth was succeeded by Franz Reichleitner, Stangl stayed on as Reichleitner's deputy. During his brief posting to Bernburg Euthanasia Centre Stangl reorganized the office at that T-4 facility. In March 1942, Stangl was given a choice to either return to the Linz Gestapo or be transferred to Lublin for work in Operation Reinhard. Stangl accepted the posting to Lublin in the General Government, where he would manage Operation Reinhard under Odilo Globočnik.