His whereabouts are then unknown over the next twelve years-even the Yagyū clan's secret chronicles, which contained lengthy passages on numerous members, has little solid information on Jūbei-until Yagyū Jūbei reappears at the age of 36 at a demonstration of swordsmanship in front of the Shōgun.
Jūbei also authored a treatise known as Tsuki mi no Shou () 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.