Jones pursued higher education upon recommendation from an individual associated with the folk school. Jones earned his B.A. in English from Berea College and an M.A. from the University of North Carolina. Before joining Berea College as a faculty member, he taught in the U.S. Army and at Jefferson County Public Schools.
Jones began working at the Council of the Southern Mountains in 1958 and served as the organization's executive director from 1967 until 1970. From 1970 to 1993, Jones directed Berea College's Appalachian Center. He was considered the "father of modern Appalachian studies". Jones also led the Celebration of Traditional Music at Berea from 1973 to 1993. In 2008, the center was named the Loyal Jones Appalachian Center after him. Jones was inducted into the Kentucky Writers Hall of Fame in 2022.
Loyal Jones was married to Nancy Swan with whom he had three children.