After the destruction of the Takeda clan, the lands came under the control of Tokugawa Ieyasu and were ruled by Suganuma Sadatoshi, followed by Mori Hideyori, and Kyōgoku Takatomo.
The domain's finances were never in good condition, and the situation continued to deteriorate over the years leading to widespread rioting in 1762 and in 1809.
The 10th daimyō, Hori Chikashige was a close supporter of Mizuno Tadakuni and held important posts within the Shogunal government, including rōjū.
During the Bakumatsu period, the domain lost another 2,000 koku for failing to stop passage of anti-government forces through its territory during the Mito rebellion.
Under the new Meiji government, Hori Chikahiro, the last daimyō of Iida Domain was given the kazoku peerage title of shishaku (viscount).