During the battle of Sekigahara, Tomoharu advanced past (stole a march on) Hideyasu, earning him Ieyasu's displeasure, and when Hideyasu's fief was transferred to Echizen, Tomoharu was hounded to become a vassal of Kamisada (the heir of the Oda clan), Hideyasu's younger brother who was also in service to him, and left the service of the Yuki family.
関ヶ原の戦いに際し、秀康に先駆け（抜け駆け）を薦めたことが家康の逆鱗に触れ、秀康の越前転封に際し、同じく秀康に仕えていた弟・守治（小田氏としては嫡男）の家臣になることを迫られて結城家を退去した。