On May 1st, the regiment fought at the Battle of Port Gibson, where it and the 3rd Missouri Infantry Regiment charged the Union line in an attempt to turn the enemy's exposed flank. However, the two regiments missed hitting the Union line on the flank, and instead hit an area with greater support. After heavy fighting, the two regiments were forced to retreat. On May 16th, the regiment joined a large assault in the Battle of Champion Hill. The Confederate charge at Champion Hill captured two important battlefield features, but Union reinforcements and a lack of ammunition forced the men to retreat. After being routed at the Battle of Big Black River Bridge on May 17th, the regiment entered the defenses of Vicksburg, Mississippi. During the Siege of Vicksburg the regiment helped repel Union attacks on May 19th and 22nd. On June 25th and July 1st, the regiment opposed Union attempts to break the Confederate lines by detonating black powder beneath the Confederate defensive works. The Confederate garrison of Vicksburg surrendered on July 4th, and the men of the 5th Missouri Infantry were paroled. After being exchanged, the 5th Missouri Infantry was combined with the 3rd Missouri Infantry to form the 3rd and 5th Missouri Infantry Regiment (Consolidated); the 5th Missouri Infantry ceased to exist as a separate unit.