When in the fall of 1918 local outbreaks of pandemic influenza occurred, Armstrong was a member of the investigating team. From 1919 to 1921, he worked as an Epidemiological Aide to the Ohio State Department of Health. For the next decades, from 1921 until his retirement from active duty in 1950 he worked at the "Hygienic Laboratory", remaining there through its administrative and name changes to the National Institutes of Health. From 1950 to 1963, Armstrong continued at the Institute, doing daily research work without compensation.