At seventeen in 1963, Lyon was again cast as a seductive teen in John Huston's The Night of the Iguana (1964), competing for the affections of Richard Burton's defrocked alcoholic preacher against the likes of Deborah Kerr and Ava Gardner. Again, controversy surrounded her because of a provocative scene in the film in which Lyon is shown emerging from the water. In 1965, she played a mission worker in China in director John Ford's last feature film, 7 Women. Lyon played the female lead in the 1967 comedy The Flim-Flam Man and had a supporting role in 1967's Tony Rome which starred Frank Sinatra. She played the wife of daredevil Evel Knievel in the 1971 film Evel Knievel.

Sue Lyon's stardom deteriorated rapidly and by the 1970s she was relegated to mainly secondary roles but continued to work in film and television until 1980.