Although initially an opponent of secession, when the American Civil War broke out, West became a brigadier general in the Mississippi State Militia. He raised a regiment, and later assumed various administrative offices for the state. Sometimes simultaneously, he served as quartermaster-general, paymaster-general, and commissary-general of the Mississippi militia. At his direction, the legislature established a commission consisting of one lawyer and two businessmen to examine and audit the books and papers of his several offices. At the end of the war, West was the only officer of the state to make a final accounting. After 1864, West also served as president of the Mississippi Central Railroad. After the war, the railroad was sold to the Illinois Central, and West was returned to the State Senate.