In 1863, the new regiment fought at the Battle of Grand Gulf, the Battle of Champion Hill, the Battle of Big Black River Bridge, and the siege of Vicksburg, where the regiment was captured as part of a Confederate surrender. The men of the regiment then underwent a prisoner exchange and rejoined the Confederate army, still under the designation of the 1st and 4th Missouri Infantry Regiment (Consolidated). In 1864, the regiment was engaged at the Battle of New Hope Church, the Battle of Kennesaw Mountain, the siege of Atlanta, the Battle of Allatoona, and the Battle of Franklin. On May 9, 1865, near the end of the war, the 1st and 4th Missouri Infantry (Consolidated) surrendered at the Battle of Fort Blakely, ending the unit's existence.