In the turmoil of the anti-Buddhist movement, the temple became extinct because they lost their territories and their fiscal foundation, and priests of this temple had to return to secular life or become Shinto priests of Isonokami-jingu Shrine.
明治に入って廃仏毀釈の嵐の中で寺領を没収され、経営基盤を奪われた当寺は廃寺となって僧侶は還俗し、石上神宮の神官となった。