At the start of the Austro-Prussian War Clam-Gallas, still in command of I Corps, was given command of units (60.000 men) detached from "North Army", called "Iser Army" and consisting out of his own I Corps, the retreating Royal Saxon Army Corps, the Austrian brigade evacuated out of Holstein, and an Austrian light cavalry division. In the course of the War, he suffered defeats at Podol, Münchengrätz and Jičín. After reuniting his force with "North Army" under Ludwig von Benedek he reverted to command of I Corps. He was relieved of his command and replaced by Count Leopold Gondrecourt in the early morning of 3 July 1866 and thus took no part in the defeat of the Austrian main army at Königgrätz that day.