Toward the end of the Warring States period when Nobunaga ODA gained control of the area around Kyoto and mounted a political opposition to Shogun Yoshiaki ASHIKAGA, Enryaku-ji Temple took Yoshiaki's side by sheltering the Asai-Asakura coalition army, and taking other anti-Nobunaga actions.
また戦国末期に織田信長が京都周辺を制圧し、将軍足利義昭との政治的対立を起こすと、延暦寺は義昭側について浅井・朝倉連合軍をかくまうなど、反信長の行動を起こした。