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.

As an independent researcher, Francis is the author of some 80 publications, including articles, books, chapters and editions, as well as several hundred reviews, editorials and reports, totalling about 4,000 pages of work. His subjects include manuscript studies, performance practice, music analysis, pedagogy, virginal music, 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. Francis is also a very active keyboard recitalist and continuo player, and has undertaken major Bach and Tudor keyboard projects in recent years.

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