Ninna-ji Temple therefore enjoyed the protection of the Imperial family and nobles; until the Meiji period princes and members of the Imperial family served as Monzeki (chief priests), controlling all sects of Buddhism as the head of Monzeki Temples.
仁和寺はその後も皇族や貴族の保護を受け、明治時代に至るまで、皇子や皇族が歴代の門跡（住職）を務め、門跡寺院の筆頭として仏教各宗を統括していた。