Per the "Roll of the Officers and Enlisted Men of the Third, Fourth, Eighteenth and Nineteenth Kansas Volunteers," a reprint of Appendix 4 to the Kansas Adjutant General's Thirteenth Biennial Report, Bowles was mustered in as First Lieutenant of John E. Stewart's cavalry company (company K) of the Third Kansas on July 24, 1861, and transferred to Company C of the Ninth when the Third and Fourth were consolidated in April 1862.

A letter from "Epaphroditus" in the October 11, 1861 Leavenworth Daily Conservative indicates Bowles went to Independence MO and forced the release of a man who had been held there for two years on the charge of helping runaway slaves, and on his return to camp Bowles helped 22 slaves escape. He was tried by a courtmartial, the results of which I don't know.

Henry Miles Moore's diary lists Bowles as one of a number of men who were tried and convicted by courts martial in the first two weeks of January 1862; unfortunately the nature of the charge and the sentence were not stated.