When the Civil War began in 1861, Humes chose to follow his home states and the Confederate cause. On March 16 he was appointed a first lieutenant in the Confederate Regular Artillery, on May 13 he was commissioned a first lieutenant in the volunteer forces, and that June was promoted to captain of artillery. Humes was posted to the Confederate fortifications protecting the Mississippi River near New Madrid, and was given command of the artillery guns there. He was still part the garrison when it surrendered, and was captured by Union forces on April 7. Humes was imprisoned at Johnson's Island located in Sandusky Bay in Ohio, until he was exchanged in September 1862.