 Matsumoto helped the Aizu Domain modernize its medical practices, and in 1868 moved to Kyoto to assist Aizu "daimyō" Matsudaira Katamori during the latter's tenure as Kyoto Shugoshoku.The situation in Kyoto was very unsettled, and Matsumoto befriended "Shinsengumi" leader Kondō Isami and rendered medical assistance to them.During the Second Chōshū expedition of 1866, he served as personal physician to the 14th Tokugawa "shōgun", Tokugawa Iemochi.