Enryaku-ji Temple occasionally caused Honmatsu disputes; it stressed that Ninnan-ji Temple was matsuji during the Kamakura period ('Gamansho' (a book that advocates orthodox of To-ji Temple's Esoteric Buddhism and counters the misleading view of the followers of Mt. Hiei)) and suppressed Kitano-tenmangu Shrine during Bunan no Koji Sodo (Riot caused by rice malt sellers in the Bunan era) in Muromachi period and Hongan-ji Temple during the Kansei adversity (religious persecution during the Kansei era) to make them accept the matsuji of Enryaku-ji.
延暦寺は他宗派の有力寺院の末寺化を目的とした本末相論を度々起こし、鎌倉時代には仁和寺を末寺であると主張（「我慢抄」）し、室町時代には文安の麹騒動で北野天満宮を、同じく寛正の法難で本願寺を屈服させて延暦寺の末寺であることを認めさせた。