The temple was later destroyed by fire on numerous occasions, including during the Onin War, and was relocated to northern Kyoto (present-day Iwakura, Sakyo Ward, Kyoto City) and central Kyoto before being restored at its current site in 1676.
その後、応仁の乱に巻き込まれるなど、数度の火災によって焼失し、寺地も洛北（現・京都市左京区岩倉）や洛中を転々とするが、1676年（延宝4年）に現在地に再興された。