In the same year of 1564, Yoshiteru utilized the Miyoshi clan in driving Sadataka ISE, then head of Mandokoro (the government administrative office) who had been hostile to the Shogun, into death in a losing battle; appointed his (Yoshiteru's) cousin-in-law Harukado SETTSU as new head of Mandokoro; strengthened his control of official decisions of the Bakufu through the Mandokoro, previously out of his real authority but now more at his mercy, and thereby steadily achieved direct rule by the Shogun as the wisest leader after Yoshimitsu ASHIKAGA.
また、三好氏を利用して永禄7年（1564年）には敵対していた政所執事伊勢貞孝を敗死に追い込み、新たな政所執事に義輝の義従兄弟にあたる摂津晴門を起用し、従来将軍の意向が及ばなかった政所を掌握して幕府決裁に対する影響力を強め、義満以来の聡明な将軍として幕府の将軍親政を着実に進めていった。