Although prosperous in its early years, the domain was hard hit by famine caused by droughts and floods during the Kanbun and Enpo eras (1661–1680), and financial difficulties continued thereafter.

Matsudaira Sadahide was severely criticized by this shogunate for mismanagement when it was revealed that although 3500 commoners had died of starvation, his samurai continued to enjoy lives of dissipation.

Despite constant financial issues, the tenshu of Matsuyama Castle was rebuilt in 1854 by the 12th daimyō, Matsudaira Katsuyoshi, although it had been destroyed by lightning seventy years previously in 1784.

In 1859, Matsudaira Katsunari, the 13th daimyō, was ordered by the shogunate to construct coastal artillery batteries at Kanagawa in Musashi Province in response to the Perry Expedition.

During the Boshin War, he guarded the Umeda area of Osaka, but on hearing that Shogun Tokugawa Yoshinobu had abandoned his forces during the Battle of Toba-Fushimi, returned to Matsuyama.