The Tokugawa shogunate reassigned the clan to the newly created 10,000 koku Yashima Domain in the inhospitable foothills of Mount Chōkai in central Dewa Province, where Ikoma Takatoshi was ordered to remain under house arrest for over 20 years.
In 1780, shōgun Tokugawa Ieharu allowed the head of the clan to visit his holdings under the sankin-kōtai system.
During the Boshin War, the Ikoma clan initially signed the Ōuetsu Reppan Dōmei agreement, but quickly switched sides on the approach of the forces of pro-Imperial Shinjō Domain.
The new Meiji government rewarded the Ikoma for their quick defection from the Ōuetsu Reppan Dōmei in 1868 with an increase in revenues to 15,200 koku, restoring the clan to the ranks of the daimyo after 250 years.
In 1884, the adopted son of the final daimyo was granted the title of baron (danshaku) in the kazoku peerage.