During the Muromachi period the temple became embroiled in political problems with the traditional temples Enryaku-ji Temple and Onjo-ji Temple and the Kanre Yoriyuki HOSOKAWA stepped in to mediate.
室町時代には旧仏教勢力の延暦寺や園城寺と対立して政治問題に発展、管領の細川頼之が調停に乗り出している。