In 1954 Mahon accepted a teaching position in the history department at the University of Florida. His interest in Military history and the Seminoles led to his three books, as well as numerous articles for encyclopedias and historical journals.
His work "History of the Second Seminole War" is considered by some as the authoritative modern reference on the little known but regional and nationally important last great war of Indian Removal east of the Mississippi. Mahon documents the American, Seminole and Black cultures, leaders, and tactics of the war.
He served as the chairman of the History Department at the University of Florida from 1965 to 1973.
After retiring in 1972, Mahon continued to pursue his interest in history. In addition, he was a founder of the Alachua Audubon Society and Florida Defenders of the Environment. He also held leadership positions in the local Sierra Club, the Florida Historical Society, and the Seminole Wars Historic Foundation.