Ordered to commit ritual suicide by Hideyoshi on February 28, 1591, at age 70. Multiple theories for the cause: (1) placing his own statue atop Daitokuji's Sanmon gate angered Hideyoshi, (2) allegations of selling cheap tea utensils at inflated prices, (3) political opposition to Hideyoshi's Korean invasion, (4) refusal to give his daughter as Hideyoshi's concubine, (5) conflict with Ishida Mitsunari over Sakai trade interests. His death poem reads: "I raise this sword / That cuts through Buddhas and patriarchs alike." His head was reportedly displayed at Ichijo-Modori Bridge, stepped upon by his own statue.

In 1591, Sen no Rikyu was ordered by Toyotomi Hideyoshi to commit seppuku, and his grave was established at Jukoin, the temple he had long designated as his family temple. Following their falling out and Rikyu's death, Jukoin became the bodaiji of the three Senke tea schools, remaining a spiritual center of tea culture ever since.