After leaving the army Schmidhuber worked as a brewer and became active in politics in Bavaria, joining the Bayerische Volkspartei (Bavarian People's Party).

From 28 November to late December 1943, then from 11 January to early February 1944 he temporarily held the command of Division Prinz Eugen.

[4] In May 1944 the SS Skanderbeg contributed to the Holocaust when it took part in the roundup and deportation of Jews from Kosovo to the Bergen-Belsen concentration camp where almost all of them perished.

[8] After six months in existence, following mass desertions within its ranks, poor combat record and history of atrocities, the division was ordered disbanded on 1 November 1944 by Heinrich Himmler.

[citation needed] Following the German evacuation of Albania, on 21 January 1945 Schmidhuber replaced SS-Brigadeführer Otto Kumm as commander of the 7th SS Volunteer Mountain Division Prinz Eugen.

The German cadres of the 21st division (Reichsdeutsche and Volksdeutsche) were absorbed into the SS-Freiwilligen Gebirgsjäger Regiment 14 of Prinz Eugen which was given the honorific name Skanderbeg in memory of its sister formation, most of the Albanian Muslims were released from service.

While Schmidhuber was in command and Prinz Eugen was deployed in Dalmatia, the unit committed multiple war crimes in Split and Dubrovnik.

[10] Division Prinz Eugen fought rearguards actions against Yugoslav partisans and Russians units as part of Army Group F while the Germans were in full retreat out of the country.

[12] A Yugoslav military tribunal tried him on charges of participating in massacres, deportations, and atrocities against civilians and sentenced him to death by hanging.