Following this, Kami-dera barely managed to continue until the Enbun era (1356-1360) but both Kami-dera and Shimo-dera, as with many other temples in Kyoto, were completely abandoned due to the Onin War.
その後、上寺の方は延文年間まではかろうじて存続していたようだが、他の京都の多くの寺同様応仁の乱により、上寺・下寺共に完全に廃寺となる。