However, many buildings of Daigo-ji Temple, including Sanbo-in, were lost in fires caused by fighting in the Onin War started in 1467, laying ruin to the temple.
しかし醍醐寺は1467年（応仁元年）に始まった応仁の乱の兵火に巻き込まれ、三宝院を含む多くの建物が焼失し、一帯は荒廃してしまう。