Hobby was an ardent supporter of states rights and organized a chapter of the Knights of the Golden Circle at St. Mary's. At the Secession Convention he represented his district and voted for secession. He was reelected to the Ninth Texas Legislature but resigned to enter the Confederate States Army. On May 14, 1862, Hobby organized the 8th Texas Infantry Battalion and was elected to the rank of major. In the next year the battalion was consolidated with other units to form the 8th Texas Infantry Regiment, with Hobby serving as its colonel. He commanded the Confederate forces at the Battle of Corpus Christi, repelling a Union invasion.