In 1922, Bowen became a Fellow in Chemistry of University College, Oxford, succeeding R. B. Bourdillon, who was briefly Fellow in Chemistry at the College from 1919 to 1921, but who subsequently changed his field of interest from chemistry to medicine. Bowen also served as Domestic Bursar of University College and as Junior Proctor of Oxford University in 1936.
Created a Fellow of the Royal Society in 1935 for his research into fluorescence, he was awarded the Davy Medal in 1963. He wrote a seminal book called The Chemical Aspects of Light. He was Vice-President of the Faraday Society and of the Chemical Society.
Much of Bowens research work was carried out at the Balliol-Trinity Laboratories in Oxford. He was an accomplished glass blower for his chemical apparatus and even produced artworks in glass. His 1966 Liversidge Lecture on Fluorescence was based on his lifes research. After retirement in June 1965, he was elected as an Honorary Fellow of University College on 6 October 1965. He was one of the longest serving Fellows of that college (43 years as an ordinary Fellow and a total of 59 years). There is a room in the college named after him. He was also a prominent Worcester Old Elizabethan serving on its Committee for many years and organising the Oxford branch of that club.
During May 1931, Bowen, then a University don, attended a series of three lectures given by Albert Einstein at Rhodes House in Oxford.  After the second lecture on 16 May, he helped rescue the blackboard used by Einstein; Sir Francis Wylie (Warden of Rhodes House) formally presented it to the Museum of the History of Science in Oxford where it remains on prominent display to this day.
As well as chemistry, Bowen also had an interest in geology, especially around Ringstead Bay on the Jurassic Coast in Dorset on the south coast of England. Perisphinctes boweni, an ammonite from the Jurassic period, is named after him. Bowen was involved with the Oxford University Museum of Natural History and produced a scale model of the sun, earth, and moon, for the upper galleries in the museum.