He moved to Kyoto to assist Aizu Domain "daimyō" Matsudaira Katamori during the latter's tenure as Kyoto Shugoshoku and helped modernize its medical practices. Matsumoto also 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.