McCown was appointed colonel of the consolidated regiment, Waddell retained his rank of major, and Bevier was transferred to Richmond, Virginia to perform recruiting duty. Companies A, C, F, and G of the new regiment contained men from the 5th Missouri Infantry, and Companies B, D, E, and H contained men from the 3rd. On October 16, 1863, the 3rd and 5th Missouri Infantry (Consolidated) transferred to Meridian, Mississippi before moving to Mobile, Alabama in January 1864. After being stationed at Meridian, Demopolis, and various locations in northern Alabama, the regiment entered Georgia in May. By that point, only 340 men remained in the consolidated regiment. In May, the regiment fought at the Battle of New Hope Church before fighting at the Battle of Kennesaw Mountain in June. Later, the regiment defended Atlanta, Georgia during the Siege of Atlanta before abandoning the city in September. The 3rd and 5th Missouri Infantry (Consolidated) lost 123 men during the Atlanta Campaign. On October 5th, the regiment was part of a Confederate attack against a Union outpost in the Battle of Allatoona, a fight which cost the regiment 76 casualties. On November 30th, the consolidated regiment was nearly annihilated at the Battle of Franklin, losing 113 out of approximately 150 men. In February 1865, the regiment transferred to Mobile, where it surrendered on April 9th during the Battle of Fort Blakely, ending the men's combat experience.