In 1948, president J. Hillis Miller of the University of Florida tapped Allen to be the university's new vice president; Miller had previously worked with Allen in the New York Department of Education. When Miller died unexpectedly in 1953, Allen became the interim president of the university. After his permanent successor, J. Wayne Reitz, assumed office in 1955, Allen continued to work as the executive vice president of the University of Florida until 1957. During his time at Florida, he was intimately involved in the planning of the university's new state medical school, teaching hospital and health science center complex.