Guibor, like many state militiamen, were arrested in the seizure of Camp Jackson in St. Louis by Nathaniel Lyon, but was soon paroled.

Guibor eventually traveled southeast from St. Louis and joined Governor Claiborne Fox Jackson's Missouri State Guard.

Guibor was wounded in an artillery duel with a Federal river squadron in the Battle of Grand Gulf.

His battery joined with John Bell Hood's army in the sweep north into Tennessee and was engaged in the battles of Franklin and Murfreesboro.

Finally, Guibor and his men surrendered with remnants of Joseph E. Johnston's army in North Carolina on April 26, 1865.