The guards were members of the SS-Totenkopfstandarte Ostmark (SS-Skull Standard), which was a new formation created in 1938. They surrounded the camp and had the order to shoot without warning at any prisoner approaching their cordon.

The northern German SS-Sturmbannführer (SS-Storm Command Leader) Albert Sauer, who earlier on had been stationed at the Sachsenhausen concentration camp, became the first commander of the Mauthausen concentration camp. In mid-February 1939 he was replaced by the Munich-born SS-Hauptsturmführer (SS-Head Storm Leader) Franz Ziereis, who previously had been commander of the 3rd SS-Totenkopfstandarte Thuringia. He held his post in Mauthausen until the liberation of this camp. With the number of concentration camp inmates steadily increasing, so did the number of SS-members. Together with the functional changes of the Mauthausen concentration camp and the creation of a large network of subcamps that brought about an enormous increase in inmates, the number of SS and Wehrmacht members rose from around 6000 in the winter of 1944/45 to almost 10,000 toward the end of March 1945.