At the outbreak of war Deisenhofer served in the SS Totenkopf Standarte, which was responsible for the police and security measures during the Invasion of Poland. After the Polish campaign, his unit was absorbed into the newly formed SS Division Totenkopf, where he served as a battalion commander during the Campaign in the West, receiving the Iron Cross First Class for his bravery in combat. In May Deisenhofer was appointed commander of a battalion of the newly formed Dutch and Belgian volunteer formation "SS Volunteer Standarte Nordwest".