Immediately after the war in 1947 he briefly attended North Texas State University where his first organ teacher, Helen Hewitt, directed him to the field of musicology.

His critical study of that composer, Gesualdo: The Man and His Music (1973), which carries a Preface by Igor Stravinsky,[2] was a 1974 National Book Award nominee.

In 2005, he was awarded the Premio Internazionale Carlo Gesualdo and was elected as an Honorary Member of the American Musicological Society.

His most recent work, The Gesualdo Hex (2010) traces not only the recognition accorded to a Renaissance prince from his own time to the early twenty-first century but places it within the context of ongoing historiographic debates and controversies.

Watkins lectured widely in America for universities, orchestras and art organizations, and his interest in both late Renaissance and 20th-century studies was reflected in numerous invited papers for international conferences as well as in projects for Columbia, Nonesuch, Pye, Éditions de l'Oiseau-Lyre, Harmonia Mundi, Glossa, and Deutsche Grammophon records and for BBC, German, and Italian television.