As Kiyomizu-dera Temple had been ruled by the Kofuku-ji Temple for a long time since the Heian period, it was frequently involved in the conflicts of the 'Nanto Hokurei,' conflict between Buddhist temples in the Nara area and Enryaku-ji Temple on Mt. Hiei, and was burnt down due to the intrusion committed by warrior-monks of Enryaku-ji Temple in 1165.
平安時代以来長らく興福寺の支配下にあったことから、興福寺と延暦寺のいわゆる「南都北嶺」の争いにもたびたび巻き込まれ、永万元年（1165年）には延暦寺の僧兵の乱入によって焼亡している。