In the midst of the Onin War on the 4th day of the 8th month of 1468, the temple was burned to the ground along with others including Shoren-in Temple during the Western Army's assault on Okazaki, and its reconstruction had not yet been completed when the temple was once again destroyed by fire on January 24, 1531 after becoming embroiled in the conflict between Takakuni HOSOKAWA and Harumoto HOSOKAWA over the position of Kanrei (Shogun's Deputy).
応仁の乱最中の応仁2年（1468年）8月4日の西軍による岡崎攻撃によって青蓮院などとともに焼失、更にその再建がままならないままの享禄4年（1531年）1月21日には今度は管領の座を巡る細川高国と細川晴元の戦いに巻き込まれて再度焼失した。