During the American Civil War, although some of his sons enlisted on opposing sides and West Virginia was created, he continued to serve as a federal judge in Union-held territory.

He moved his young family westward in Virginia along the Midland Trail, establishing his own farm and legal practice in Cabell County near the confluence of the Mud and Guyandotte Rivers.

His eldest son, Elisha W. McComas (1822-1890), who had served in the U.S. Army during the Mexican-American War, won election as Lieutenant Governor of Virginia in the following decade, but resigned because of how Governor John S. Wise handled the aftermath of John Brown's raid on Harper's Ferry.

On September 4, 1862, his third son, Hamilton Calhoun McComas (1831-1883, and another lawyer) enlisted in the Union Army in Illinois, and served for several months before resigning.

His youngest son, Benjamin McComas (1836-1894), enlisted in the 30th Virginia Sharpshooters, a Confederate unit, but survived the war.