Later, when the castle was attacked by the ninth Shogun Yoshihisa ASHIKAGA, twice, in August and September, due to Takayori ROKKAKU's invasion of bakufu goryochi (the land directly controlled by bakufu [Japanese feudal government headed by a shogun]), they temporarily abandoned the castle, conducted guerrilla wars in the mountains of Koka, and recaptured the castle later in both wars (the Chokyo-Entoku Wars).
その後、六角高頼が幕府御料地を侵略した際には9月と8月の2回、第9代将軍足利義尚の親征を受けたが、その2度とも観音寺城を放棄し甲賀の山中でゲリラ戦を展開、一時的に城を明け渡すが共に奪回している（長享・延徳の乱）。