Several hundred (2500?) Guardsmen transferred east of the Mississippi River following Pea Ridge. Once there many transferred to the Confederate army. Gen. M. M. Parsons led a few hundred (800?) back to the Trans-Mississippi department in July, 1862. These men would be ordered into the Confederate army in September, 1862, per the following letter:

Hd Qrs Trans Miss: Dpt.
Little Rock
Sept. 24th 1862.

Genl: I am instructed by the Genl Comdg today that yourself and Command have been turned over by Gov Jackson to the Confederacy just as you are and will be recognized accordingly and will be so reported in the war Department.

Very Respectfully (Signed)
Your srvt
James Deshler
Capt A.A.A.S.

A few Guard officers attempted to maintain state organizations by recruiting new units in August - September, 1862, but they were likewise incorporated into Confederate service in September.

Some stray Guard units remained in service, including a number under Gen. James Rains, until late 1864, but the majority of the Missourians served in regular Confederate units after September, 1862.

Suggested reading on this subject is Wayne Schnetzer, Tried Soldiers Full of Zeal for the Cause: A Brief History of the Missouri State Guards after Pea Ridge, March 9, 1862 - Spring of 1865 (Independence, MO: Two Trails Publishing, 2011).