Karl Haushofer appears in the anime movie *Fullmetal Alchemist: Conqueror of Shamballa*, continuing the 2003 series' story. Retiring from the German army, he became a University of Munich professor in 1921. There, he encountered the newly arrived Van Hohenheim. Impressed by Hohenheim's vast alchemical knowledge, Haushofer secured his entry into the secretive Thule Society, believing it could help Hohenheim return his son, Edward Elric, to his original world.

Deeply involved in the Thule Society, which merged occult beliefs with political ambitions tied to the rising Nazi movement, Haushofer manipulated Alfons Heiderich's rocket research. His aim was to use the technology to open a portal to Amestris, the parallel world, requiring a massive alchemical sacrifice. Though initially allied with Hohenheim, Haushofer betrayed him, permitting the Thule Society to sacrifice Hohenheim in their ritual to reach Shamballa—their term for the gateway to Amestris.

After the ritual failed, resulting in Hohenheim's death and Edward Elric's brief return to Amestris, Haushofer's direct involvement ended. He was last seen observing from a distance as the Thule Society collapsed following their unsuccessful coup attempt alongside Adolf Hitler's failed Beer Hall Putsch.