After spending the summer of 1863 harassing Union Navy shipping on the Mississippi River, the regiment was reorganized, with elements of an Arkansas unit being replaced with the 8th Missouri Infantry Battalion.

[1] At the Battle of Prairie Grove on December 7, Roane's brigade contained four cavalry regiments from Texas and two artillery batteries from Arkansas, in addition to Clark's Missouri Infantry.

[6] Clark's Missouri Infantry hit the right flank of Colonel William A. Weer's brigade, but heavy Union artillery fire blunted the charge.

Not long afterwards, the regiment boarded the Granite State for transfer to Day's Bluff, Arkansas, where it encamped at Fort Pleasant.

[10] On June 12, Clark's brigade began a raid to the Mississippi River, with the intention of harassing Union Navy shipping.

The brigade, including Clark's Missouri Infantry, attacked a gunboat and several transport vessels on June 22, causing some damage.

In late July, the regiment built fortifications designed to protect Little Rock, which was threatened by Union Major General Frederick Steele.

[12] The new regiment was then assigned to the brigade of Brigadier General Thomas F. Drayton, with which it transferred to Camp Bragg on October 20, where it spent the rest of 1863 in winter quarters.

Parsons' division left Shreveport on April 3 to come to the aid of Major General Richard Taylor, who was resisting a Union advance up the Red River.

Between the thick mud and a counterattack by the 2nd Kansas Colored Infantry Regiment, the Confederate attack was unable to crack the Union line.

Jenkins' Ferry was the last major combat action the regiment saw; the unit spent the rest of the war stationed at various points in Arkansas and Louisiana.

On June 7, 1865, the survivors of the regiment were paroled at Alexandria, Louisiana; the steamboat B. L. Hodge transported the men back to Missouri.