When growing tensions between the north and south caused the State of Texas to increase the size of its militia, Robert was elected Colonel of the 17th Texas Brigade of State Troops. In July 1861, Powell resigned his commission in the 17th Brigade and was elected Captain of a company of volunteers known as the "Waverly Confederates", which became Company D of the 5th Texas Infantry. The 5th Texas Infantry traveled to Virginia and arrived in September, 1861.

After arriving in Virginia, Colonel James J. Archer was appointed commander of the 5th Texas in a brigade which included the 1st & 4th Texas Infantry and the 18th Georgia Infantry. This brigade was placed under the command of Brigadier General John B. Hood in December, 1862 and would become known as "Hood's Texas Brigade". In April, 1863, Robert Powell was promoted to Colonel and commander of the 5th Texas Infantry Regiment after its temporary commander Captain Ike Turner was killed. Colonel Powell led his regiment in battle of Gettysburg, July 1-3, 1863. After a brutal assault on Little Round Top by the 4th and 5th Texas Infantry, US Colonel Joshua Chamberlain found the wounded body Colonel Powell among the boulders. He was sent to the 83rd Pennsylvania where he was taken prisoner. Powell spent several weeks in the field hospital and then was transferred to a prison camp at Ft. McHenry and later to Johnson's Island on Lake Erie. He was finally exchanged on February 6, 1865 and returned to the "Texas Brigade" and served as it's last commander until the end of the war. Though the brigade had dwindled to approximately 700 from the original 5,300 soldiers, the "Texas Brigade" was still a respected fighting unit. When Lee's army surrendered at Appomattox, only 11 of Company D's original "Waverly Confederate's" remained.

Robert M. Powell, his second wife and 2 children moved to St. Louis, Missouri in 1882 where he lived until his death on January 15, 1916. He is buried in Calvary Cemetery in St. Louis.