Flowers was first employed as instructor for Trinity while the college was still in Randolph County. As an engineer, one of his first responsibilities was to wire the new buildings in Durham for electricity after the move in 1892. Affectionately known by students and alumni as "Professor Bobby Flowers," he was named president of Duke University following the death of President Few in 1941. His experience and stature were welcome because the demands of a world at war and the strains of transition to a peacetime economy dominated every aspect of university life during his presidency. In 1948, he stepped down as president and served as chancellor until 1951.