From November 1939 until the end of World War II, he commanded the Concentration Camps Inspectorate, later integrated into the SS Main Economic and Administrative Office as "Amt D".

When World War I broke out, Glücks returned to Germany under a false identity on a Norwegian ship in January 1915 and joined the army again.

[5] Glücks made few changes once taking over, leaving the organizational structure intact as Eicke had set it up; the same uncompromising rigidity was carried out at the camps—there was no rehabilitation and no effort to exploit the working potential of inmates.

At the same time, it was Glücks who recommended on 21 February 1940, Auschwitz, a former Austrian cavalry barracks, as a suitable site for a new concentration camp to Himmler and Reinhard Heydrich.

[15] Just a few days after the Wannsee Conference in January 1942, Himmler ordered Glücks to prepare the camps for the immediate arrival of 100,000 Jewish men and 50,000 women being evacuated from the Reich as labourers in lieu of the diminishing availability of Russian prisoners.

Correspondingly, Auschwitz Kommandant Rudolf Höss routinely informed Glücks on the status of the extermination activities.

[21] During one of his inspection-tour visits to Auschwitz in 1943, Glücks complained about the unfavorable location of the crematoria since all types of people would be able to "gaze" at the structures.

[22] When visits from high officials from the Reich or the Nazi Party took place, the administration was instructed by Glücks to avoid showing the crematorias to them; if questions arose about smoke coming from the chimneys, the installation personnel were to tell the visitors that corpses were being burned as a result of epidemics.

[25] Glücks was "the RSHA man responsible for the entire network of concentration camps", and his authority extended to the largest and most infamous of them all, Auschwitz.

[27] Glücks' role in the Holocaust "cannot be over-emphasized" as he, together with Pohl, oversaw the entire Nazi camp system and the persecution network it represented.

[9] After the capitulation of Germany, he is believed to have committed suicide on 10 May 1945 by swallowing a capsule of potassium cyanide at the Mürwik naval base in Flensburg-Mürwik, although the lack of official records or photos gave rise to speculation about his ultimate fate.