The Second Missouri Volunteer Infantry included a significant number of members with military experience from service in Europe. Many had also participated in drill and marksmanship competitions in St. Louis's many Turnverein societies. The Second Missouri was an unusually large regiment, having two dedicated "Rifle Companies" in addition to its ten companies of infantry. Upon entry into Federal service the members of the new Second Missouri elected Henry Boernstein colonel of the regiment. The new Missouri Volunteer regiments, subsequently elected (then) Captain Nathaniel Lyon as the brigadier general of the new brigade of Missouri volunteers. President Lincoln would later confirm Lyon's promotion from Captain to Brigadier general.
On May 10, 1861, the 2nd Missouri participated in the arrest of the Missouri Volunteer Militia drilling at Camp Jackson at Lindell Grove on the western border of St. Louis City. As the Missouri militiamen were being march under guard back to the Arsenal near the riverfront, angry crowds confronted the Federal forces and the confused situation soon devolved into rioting and gunfire. Over 27 people were killed and the Camp Jackson Affair helped to polarize the state and send Missouri down the road to its own internal civil war.
On June 15, 1861, the Second Missouri participated in the unopposed occupation of the Missouri state capitol at Jefferson City, Missouri, by Federal troops. Nine companies of the Second Missouri remained as the garrison at Jefferson City, under Colonel Boerstein who acted as interim military commandant of the city.
Company "B" and Rifle Companies "A" and "B" continued up river in pursuit of fugitive Governor Claiborne Fox Jackson and the Missouri State Guard. At Boonville the three company battalion of the Second Missouri, fighting under the command of Captain Peter J. Osterhaus helped defeat the newly organized Missouri State Guard on June 17 in the short, one-sided Battle of Boonville. While the Battle of Boonville was small by later war standards, it had major strategic consequences, driving the pro-secessionist forces into the southern part of the state and securing the Missouri River valley and communications across the state for the Federal government.
The Second Missouri garrison at Jefferson City made a number of expeditions and "scouts" into the counties near the state capital and the central Missouri River valley. A Second Missouri detachment from Jefferson City fought a small engagement with guerrillas at Mexico Missouri, on July 15, 1861.
Osterhaus' small battalion continued to campaign with Lyon, marching southwest to Springfield, eventually confronting a united Confederate and Missouri State Guard force near Springfield. The resulting Battle of Wilson's Creek fought ten miles south of the city on August 10, 1861, was a bloody affair, and the second costliest in American History up to that time. Osterhaus, by that time promoted to Major, led his men in the fighting as part of Lyon's detachment of the Federal force on Bloody Hill. Isolated and outnumbered after a second Federal element under Colonel Franz Sigel was routed, the Federals on Bloody hill fought the Confederate forces to a stalemate. The battle ended only after General Lyon was killed leading the 1st Iowa Infantry against the Confederate right. As the senior U.S. Army regular officer present, command devolved to Major Samuel D. Sturgis. Concerned about his force's ammunition supply, Sturgis decided to withdraw towards Springfield.
Osterhaus' men withdrew with the battered Federal force to Springfield, then to Rolla, continuing on to St. Louis.