On August 29, 1861, he was apprehended in Georgetown, Pettis County, Missouri by Col. Henry M. Day of the First Illinois Cavalry, after a shootout that took life of Sergeant George W. Glasgow, 1st Illinois Cavalry, and placed under arrest in Lexington. After the Battle of Lexington Magoffin was exchanged for former Missouri Governor Austin A. King and stayed with Gen. Price's army. In December 1861, he asked for and received a 10-day pass from Col. Frederick Steele, Union Army of the West to see his wife who was dying; Union military authorities assumed that Magoffin asked for and was paroled. On his return from Prairie Lea, Magoffin was taken prisoner with his two sons, Elijah H. Magoffin, 24 years old, and Beriah Magoffin, 19 years old, at Milford, Johnson County, Missouri, while traveling with a detachment of Confederate troops under Col. F. S. Robertson.