Allen was an organ scholar at Christ's College, Cambridge, and later held organist's posts at Ely cathedral (1898–1901) and New College, Oxford (1901–18). In 1918 he became director of the Royal College of Music, London, and in the same year professor of music at Oxford. He raised the position of music in the Oxford curriculum and made more adequate provisions for research and teaching, accomplishments that had wide influence elsewhere. He was also noted for his research on Heinrich Schütz and J.S. Bach. He conducted the Bach choirs in Oxford (from 1901) and London (1907–20) and was a leading proponent of contemporary English music.