On 30 January 1939 Schmidhuber was promoted to the rank of SS Sturmbannführer and put in command of the 1st SS battalion regiment Germania. On 21 June 1941 he was promoted to SS Obersturmbannführer and a year later he became the commander of the SS-Freiwilligen-Gebirgsjäger-Regiment 14 "Skanderberg" of 7th SS Volunteer Mountain Division Prinz Eugen. On 20 April 1943 Schmidhuber was promoted to SS Standartenführer (Colonel) and from 17 April 1944 until 20 January 1945, served as a commander of the 21st Waffen Mountain Division of the SS Skanderbeg (1st Albanian).