Armstrong moved to Yankton, then a small Native American village, in Dakota Territory, when Minnesota Territory was admitted as a State. He was a member of the first Territorial House of Representatives in 1861, and was reelected in 1862 and 1863, serving as speaker in 1863. He became editor of the Dakota Union newspaper in 1864, was appointed clerk of the territorial Supreme Court in 1865, and was elected to the territorial council in 1866 and in 1867, chosen as president.
He acted as secretary of the Indian peace commission in 1867. Continuing as a surveyor, he established the great meridian and standard lines for United States surveys in southern Dakota and in the northern Red River Valley. He was again elected to the Territorial council in 1869, and was elected as a Democrat to the United States House of Representatives from March 4, 1871-March 3, 1875. He was an unsuccessful candidate for reelection in 1874, and moved to St. James, Watonwan County, Minnesota, where he engaged in banking and in real estate.
Armstrong died in Albert Lea, Minnesota, and was interred in Lakewood Cemetery, Minneapolis, Minnesota.