Francis Knights was born in St John’s, Newfoundland, and educated at Royal Holloway College, University of London, graduating with a first-class degree in music. In his final year he founded and directed the college Bach Tercentenary Festival. A year as a lay clerk at Portsmouth Cathedral was followed by postgraduate research into Elizabethan music manuscripts at Magdalen College, Oxford (his thesis was a study of the Music Manuscripts of Edward Paston) where he was an academical clerk in the chapel choir; he was also director of music at Green College Music. After a year of teaching at Oxford University, he was appointed Research Fellow at the Royal Northern College of Music, then worked at the BBC and as a specialist early music discographer; during part of this period he was conductor of the Portsmouth-based ensemble The Renaissance Choir. He then spent three years in Oxford, teaching at the university and holding the position of Director of Chapel Music at Somerville College. In 2004 he held an Edison Fellowship at the British Library and was editor of Clavichord International and Discography Manager at the Centre for the History and Analyis of Recorded Music at King's College, London until 2009.

Since 2008 he has been Director of Music and Director of Studies in Music at Fitzwilliam College, Cambridge, and in October 2009 became Editor of  Early Music.

His writings include articles on cathedral music, manuscript sources, performance practice and organology for The Organ, Musical Times, Organists’ Review, Music Review, Journal of the British Institute of Organ Studies, Clavichord International, Neue Zeitschrift für Musik, Rivista Italiana di Musicologia, Galpin Society Journal, Dictionnaire de l’art vocal and The Routledge Encyclopedia of Keyboard Instruments. He has given conference papers and lectures on Elizabethan music sources, J S Bach and on early keyboard instruments, and written CD booklet notes for Hyperion and OxRecs and programme notes for the Tallis Scholars, as well as editing choral music for professional ensembles (including Brumel’s Missa et ecce terrae motus, recorded on Gimell and published by Mapa Mundi). His compositions, including choral, chamber and keyboard works, have been performed in St Paul's, Portsmouth, Lichfield, Oxford and Dublin cathedrals.

His practical studies have included harpsichord lessons with Robert Woolley and David Roblou, organ lessons with Harry Bramma, vocal studies with David Lowe, baroque flute with Duke Dobing, theorbo with Liz Kenny and Yair Avidor and viola with Gillian Ruddick. Other instruments include clavichord, fortepiano, cornett and recorder. Francis is very active as a performer, directing the Cambridge-based choir Voces Angelicae, the chamber group Le Rossignol and the professional period-instrument ensemble Bach Collegium Oxford. In 2001-4 he was conductor of the Oxford-based Renaissance vocal ensemble Gradualia. He teaches harpsichord, clavichord and organ, has led early keyboard workshops for The Bate Collection, Oxford, and Churchill College, Cambridge, and sings in numerous choirs, including deputizing in three cathedral choirs. His other interests include opera and theatre. Long-term recital projects include a complete performance of the Fitzwilliam Virginal Book in Cambridge, Oxford and London, on harpsichord, virginals, clavichord and organ, in 2005-2012.