Francis Knights studied at Royal Holloway College, University of London, Magdalen College, Oxford and Nottingham University. He has held positions at the Royal Northern College of Music, Green College, Oxford, Somerville College, Oxford, the BBC, the British Library and King's College, London, and been editor of four music journals. He is also a former Cambridge University Proctor.

Francis is the author of some 80 publications, including books, chapters, editions and articles, on subjects such as manuscript studies, performance practice, music analysis and pedagogy, virginal music, Bach, Haydn, Burney, Farnaby, early keyboard instruments and church music.

Over the years he has founded and directed many vocal and instrumental ensembles, including Gradualia, the Cambridge Renaissance Ensemble, Bach Collegium Oxford and the Erasmus Chamber Choir, and has also been conductor of Voces Angelicae, Somerville College Chapel Choir and the Renaissance Choir, among others. He is also a very active keyboard recitalist and continuo player.

Since 2009 he has been Fellow, Tutor and Director of Studies in Music at Fitzwilliam College, University of Cambridge, and is Chairman of the National Early Music Association and Editor of Harpsichord & Fortepiano.