When news of the Civil War reached Minnesota, Bloomer and his cousins joined the Stillwater Guards, a local militia group. The Guards were mustered into the First Minnesota Volunteer Infantry Regiment at Fort Snelling on April 29, 1861, forming the nucleus of Company B. Bloomer was initially given the rank of corporal and participated in all the regiment's major engagements until the Battle of Antietam. He was wounded slightly in the head at the Battle of Bull Run. During the Battle of Savage's Station on June 29, 1862, which was part of the Peninsula Campaign, Bloomer was promoted to color sergeant. In the midst of the engagement the standard bearer was killed. Bloomer picked up the colors, and was separated from the regiment for five hours. He returned the colors to the regiment and was promoted for his bravery.