Following Virginia’s secession, Nadenbousch’s company was called into service and became Co. D, 2nd Virginia Infantry, which was part of the Stonewall Brigade under General Thomas J. "Stonewall" Jackson, and first engaged at the First Battle of Manassas. Following the battle, Nadenbousch personally brought home the bodies of three of his men, and buried them in the Old Norbourne Cemetery, in Martinsburg. Later the commander of the regiment, Nadenbousch was twice wounded; first at the Second Manassas, in August, 1862, and, less than a year later, at the Battle of Chancellorsville, in May, 1863. On account of impaired health, and at his own request, Nadenbousch was relieved later that summer, from duty in the field, and assigned to the command of the post at Staunton, Virginia. He later resigned on April 12, 1864, and began his return to civilian affairs before the war concluded. In his obituary, Nadenbousch was noted for his courage, ability, and coolness; and said to be a favorite of General Jackson.