On July 4, 1863, the regiment, as part of Brigadier General Mosby M. Parsons' brigade, broke through the Union lines at the Battle of Helena.

However, Governor Claiborne F. Jackson, who supported secession, organized like-minded state militia into a camp outside of St. Louis.

On May 10, Nathaniel Lyon, a brigadier general in the Union Army, dispersed Jackson's camp, although a riot in St. Louis followed.

Lyon took Boonville two days later by forcing out a group of Missouri State Guard soldiers led by Colonel John S. Marmaduke.

[2] After Wilson's Creek, Price and the Missouri State Guard moved north, capturing a Union garrison at Lexington after a siege in September.

[4] In November, Jackson and the pro-secession legislators held a vote approving secession while at Neosho; Missouri joined the Confederate States of America as a government-in-exile.

[5] In February 1862, Union pressure led Price to leave Missouri for Arkansas, where he joined forces with Major General Earl Van Dorn.

[6] In March, Price joined the Confederate States Army, receiving a commission as a major general.

[7] Later that month, Van Dorn was defeated at the Battle of Pea Ridge, establishing Union control of Missouri.

Ponder commanded the regiment during the movement, as White was ill.[13] During the early stages of the Battle of Prairie Grove on December 7, the regiment (under the name Ponder's Missouri Infantry) aligned with the rest of Parsons' brigade in a position supporting the Confederate left flank.

[21] On July 4, the 9th Missouri Infantry was part of a Confederate assault against a Union force occupying Helena, Arkansas.

After a five-hour fight, the Confederates were driven back from Graveyard Hill with heavy losses, including many men captured.

[22] Beginning in August, the regiment built fortifications designed to defend Little Rock against Union attack.

[22] The unit reached Taylor's position on April 9, and fought in the Battle of Pleasant Hill later that day.

[28] After a brief rest, the regiment then began moving north towards Camden, Arkansas, which was held by Major General Frederick Steele's Union force.

[28] At the Battle of Jenkins' Ferry on April 30, Parsons' division deployed at around 10:00 a.m., having arrived on the field an hour earlier.

On September 29, the regiment was officially consolidated into the 10th Missouri Infantry while stationed in Arkansas, ceasing to exist as a separate unit.