Following the dawn of the sixteenth century, amid the turmoil of Sengoku, the Honganji Buddhist sect engaged its activities in various regions in Japan using its power of organization, which was constituted by petty peasants up to samurai hierarchy such as the local samurai, the local ruling families and so on; however, in 1532 Yamashina Honganji Temple suffered damage due to the Tenbun-hokke-no-ran War, and therefore the tenth generation (Shonyo) moved to Ishiyama Gobo, which was opened in Nishinari-gun, Settsu-no-kuni (currently Osaka City) by Rennyo, which became Ishiyama Honganji Temple.
16世紀に入ると、戦国の動乱の中で、本願寺教団は零細な農民から地侍、土豪などの武士階層に至るその組織力を武器に日本各地で活動を活発化させるが、山科本願寺は天文法華の乱により1532年に戦災にあい、第10代証如は摂津国西成郡（現在の大阪市）に蓮如が開いた石山御坊へと移り、石山本願寺とする。