Nicholls initially opposed the idea of secession, but after the Louisiana Secession Convention voted in favor of leaving The Union and later joined the
Confederate States, he volunteered for military service. He and his brother Lawrence formed an infantry company from volunteers in
Ascension Parish named The Phoenix Guards. The company was made part of the
8th Louisiana Infantry Regiment under the command of Colonel Henry B. Kelly with Nicholls being made Lieutenant Colonel. He trained the regiment and gained a reputation as a stern drill master and disciplinarian. The 8th Louisiana was deployed to Virginia and put on guard duty during the
Battle of Bull Run. The regiment was then put under the command of General
Richard Taylor. In Spring 1862, Nicholls and his regiment participated in the
Valley Campaign of General
Stonewall Jackson. Jackson sought to capture the town of Winchester from Union troops and on May 25 ordered Taylor to take a ridge which was heavily defended. As Taylors brigade reached halfway up the ridge a Union cavalry charged attacked their left flank, which was occupied by the 8th Louisiana. Nicholls was ordered to withhold slightly, and they were able to repulse the cavalry charge. While perusing the enemy, Nicholls had to cross two stone fences which exposed him to heavy fire, and he was shot in the left arm which shattered his elbow. After the Confederates took the town, Nicholls was left behind to recover as his injuries required that his left arm be amputated. After Jackson led his troops to continue the campaign, Union forces reentered Winchester and Nicholls was taken prisoner but later released in a prisoner exchange on September 21, 1862. While on leave for a period of four months, Nicholls was promoted to Colonel and then to Brigadier General and given command of 2nd Louisiana Brigade. He was ordered to report to General
Robert E. Lee then stationed in Fredericksburg, Virginia. When the
Army of the Potomac under the command of
Joseph Hooker launched a campaign to push Lee out of Fredericksburg, Nicholls was ordered to participate in a flanking maneuver to attack Hooker's right at
Chancellorsville. While leading his brigade and attempting to clear obstacles in their path, Nicholls positions came under artillery fire. A shell cut through his horses' stomach, came out the other end, and severed his left foot. After being evacuated to the rear by his men, Nicholls retired from field command for the remainder of the war. After a second convalesce leave, Nicholls was given administrative duties and named the Commandant of the Military District of Lynchburg, Virginia on August 11, 1863. Lynchburg, located west of Richmond, was an important railroad junction for supply routes. He was relieved of command in the summer of 1864 and transferred to the
Trans-Mississippi Department in Marshall, Texas. He remained here until the end of the war. In 1874, while testifying before a Congressional Committee investigating election fraud in Louisiana, Nicholls said of his service in the war; "I think that we made the attempt [the war for secession] under the most favorable circumstances...of course we all regret our want for success; but I do not believe that there is anywhere any desire for a renewal of the attempt." and that "My war record is a source of private misfortune without a corresponding gain to anyone. My services to my country were not worth the price to me. Every battle I went into I was wounded, and so I could not serve all the time." ==Political career==