Jien resided in the temple in the early Kamakura period and at this time, the temple name was changed its first chinese character from 良 to 善 after receiving a temple name tablet written by Emperor Go-Toba himself.
鎌倉時代初期には慈円が住したことがあり、このころ後鳥羽天皇直筆の寺額を賜ったことによって寺号が善峯寺と改められた。