From the beginning of the Boshin War, the Ii Family showed their loyalty to the Emperor by guarding To-ji Temple and the town of Otsu with soldiers of the Satsuma clan at the Battle of Toba-Fushimi and, having achieved great success with the arrest of Isami KONDO, were rewarded with territory worth 20,000 koku.
戊辰戦争の際には、すでに鳥羽伏見の戦いの時点で薩摩藩兵とともに東寺や大津を守備するなど、最初から勤王の姿勢を示しており、近藤勇を逮捕する手柄を立てるなど実戦での功績も評価され、賞典禄2万石を与えられている。