On the outbreak of the American Civil War Soule enlisted with the 13th Regiment Massachusetts Volunteer Infantry serving the Union Army.

He was wounded at the Battle of Antietam on September 17, 1862, and served out the remainder of the war with the Veteran Reserve Corps.

When his business was destroyed in a fire in early 1867 he moved west to Fort Dodge (United States Army Post) in Kansas where he found work as a clerk in the sutler's store and the following year moved on to Fort Supply in Indian Territory.

Will Soule documented the construction of the fort, but is primarily known for his high quality portraits and photographs of Native American subjects.

That year he was married to Ella Augusta Blackman, resided for a time in Philadelphia, then moved to Vermont and finally in 1882 to Boston where he took over the business of his older brother, John P. Soule, The Soule Art Company while the latter was moving to Seattle.