In August 1941, Deisenhofer was transferred to the command of the Regiment "Germania", one of the Infantry regiments of the SS Division Wiking, currently serving on the Eastern Front. Deisenhofer was sent back to the Totenkopf division in February 1942 as a regimental commander. The division was encircled in the Demyansk Pocket, where he commanded a battle group during the breakout, receiving a Knight's Cross of the Iron Cross for his actions. Deisenhofer then served as an SS training officer. In March 1944, Deisenhofer was sent back to a combat formation, this time to command a regiment of the 10th SS Panzer Division Frundsberg, which took part in the operation to relieve the encircled 1st Panzer Army of Generaloberst Hans-Valentin Hube in what was known as the Kamenets-Podolsky pocket.