In 1862, Matsudaira Yoshinaga, a long-time political rival of Ii Naosuke, had the kokudaka of Hikone Domain reduced from 300,000 koku to 200,000 koku and demanded the execution of Ii Naosuke's former chief advisors, Nagano Shuzen and Rokunojo Utsugi.

However, Ii Naonori grew increasingly dissatisfied with the continued hostile treatment still accorded Hikone Domain by the shogunal administration.

During the Battle of Toba-Fushimi, although Hikone forces were stationed at Osaka Castle, they did not join the shogunal army, but simply marched home.

The new Meiji government awarded Hikone an additional 20,000 koku shortly before the abolition of the han system.

In 1871, Ii Naonori traveled to the United States and England, during which time he was attended by Sōma Nagatane, who became the founder of Senshu University.