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Marshall accepted a commission as captain of Company M of the 1st North Carolina "Bethel Regiment" under Col. Daniel Harvey Hill in the spring of 1861. He did not take part in the Battle of Big Bethel. He received a promotion to colonel of the 52nd North Carolina on April 23, 1862 under the command of Brig. Gen J. Johnston Pettigrew, despite having no combat experience. Marshall was initially elected to the post of lieutenant colonel and Zebulon Vance was elected colonel, however, Vance declined the position so Marshall took the spot instead. Marshall defended Norfolk, Virginia from federal gunboats, then defended the Blackwater River. Pettigrew's Brigade joined the Army of Northern Virginia in late May 1863, for the Gettysburg Campaign.