According to notes made by his daughter Francis in 1923, Charles Bowers was forty-eight years old and the father of six children when he volunteered to serve as the third lieutenant in Company G of the Fifth Regiment Massachusetts Volunteer Militia, also referred to as the Concord Artillery. When his three-month term expired he returned home to Concord and began actively recruiting a company of his own. In June 1862 he once again departed Concord as captain of Company G of the Thirty-Second Regiment Massachusetts Volunteer Infantry. He served with this company until after the end of the war.

Bowers' two oldest sons also served in the Union army. Along with his father, twenty-year-old William Bowers answered Lincoln's first call for troops, enlisting as a private in the Concord Artillery. After his three months of service ended he also returned to Concord, eventually reenlisting with the Forty-Fourth Massachusetts Volunteer Militia in August 1862. He served with this regiment until he was discharged for disability in February 1863. In June 1862, Charles Bowers' second son, eighteen-year-old Charles E. Bowers, enlisted in his father's company, Company G of the Thirty-Second Massachusetts. He was wounded at Gettysburg and was eventually discharged for disability. According to his sister Francis, his death several years after the end of the war was a result of complications from the wounds he received at Gettysburg.

The Fifth Regiment Massachusetts Volunteer Militia was mustered into federal service in Washington on 1 May 1861 and remained in that city for four weeks. On 25 May the regiment transferred to a camp near Alexandria, where it remained until it marched toward Manassas, Virginia in July. After engaging in action at the First Battle of Bull Run, the regiment returned to Washington before travelling back to Boston where it was mustered out of service on 31 July 1861.