In the summer of 1861, Union general John C. Frémont arrived in St. Louis to take command of the Department of the West. Missouri's provisional government in Jefferson City had been established, and St. Louis was to be the staging ground of statewide military operations. Frémont focused on the defense of St. Louis, building ten earthwork forts around the city and constructing Benton Barracks, a spacious facility for training Federal troops, as well as accommodating wounded soldiers, freed slaves, and refugees. However, Frémont proved to be a controversial, uncooperative leader, and his tenure was brief.

After the Camp Jackson affair in St. Louis, the city saw no concerted war action. But Missouri was the scene of numerous battles, including one that summer at Wilson's Creek, where Southern forces won the day but at great cost. Most of the other pitched battles went to the Union, and the state remained firmly in Union control.