Despite not being the heir of his father as the headmaster of the Yagyū style (and thus far from being an unrivaled swordsman under the Heaven), he received the post for its importance in Japanese politics and Court intrigues, at which Munenori was better than the other members of his clan.
Following this exhibition, Jūbē was reinstated and serves for a short time as a government-inspector (御所印判, Gosho Inban), taking control over his father's lands until Yagyū Tajima no Kami Munenori's death in 1646.
Jūbē also authored a treatise known as Tsuki no Shō (月之抄) or The Art of Looking at the Moon outlining his school of swordsmanship as well as teachings influenced by the monk Takuan Sōhō who was a friend of his father's.
After residing in Edo for several years after his father's death, Jūbē left his government duties and returned to his home village where he died in early 1650 under uncertain circumstances.
Due to Yagyū Jūbē's frequent disappearances and the fact of little existing records of his whereabouts, his life has bred speculation and interest and has been romanticized in popular fiction.