| 1978 | Music of John Sheppard | John Sheppard, The Clerkes of Oxenford & Directed by David Wulstan | | 1 |
| 1981 | Masses by Tallis & Sheppard | Thomas Tallis, John Sheppard; St. John's College Choir, Cambridge, George Guest | | 2 |
| 1988 | Church Music, Volume 1 | John Sheppard; The Sixteen, Harry Christophers | | 1 |
| 1991 | Church Music by John Sheppard - 2 | John Sheppard; The Sixteen & Harry Christophers | | 1 |
| 1992 | Church Music by John Sheppard - 3 | John Sheppard; The Sixteen, Harry Christophers | | 1 |
| 1993 | Western Wind Masses | Taverner, Tye, Sheppard; The Tallis Scholars, Peter Phillips | | 2 |
| 1993 | Church Music by John Sheppard - 4 | John Sheppard; The Sixteen, Harry Christophers | | 1 |
| 1997 | 'Cantate' Mass and Other Sacred Choral Music | John Sheppard; The Sixteen, Harry Christophers | | 1 |
| 2000 | Missa Cantate | John Sheppard; Gabrieli Consort & Players, Paul McCreesh, Salisbury Cathedral Boy Choristers | | 1 |
| 2003 | Songs of Angels: Music from Magdalen College, Oxford | Davy, Mason, Appleby, Preston, Sheppard; The Choir of Magdalen College, Oxford, Bill Ives | | 1 |
| 2005 | Audivi vocem | Thomas Tallis; Christopher Tye, John Sheppard; The Hilliard Ensemble | | 1 |
| 2010 | Media Vita & other liturgical works | John Sheppard; Stile Antico | | 1 |
| 2012 | Messe "Cantate" / "Spiritus Sanctus" | John Sheppard; The Clerkes of Oxenford, David Wulstan | | 1 |
| 2013 | Gaude, gaude, gaude Maria: Sacred Choral Works | John Sheppard; Choir of St. John’s College, Cambridge, Andrew Nethsingha | | 1 |
| 2013 | J. Sheppard: Sacred Choral Works | John Sheppard; Choir Of St. John’s College, Cambridge, Andrew Nethsingha | | 1 |
| 2014 | Sacred Choral Music | John Sheppard; Choir of St. Mary’s Cathedral, Edinburgh, Duncan Ferguson | | 2 |
| 2014 | The Voice of the Turtle Dove | Sheppard, Davy, Mundy; The Sixteen, Harry Christophers | | 1 |
| 2015 | In the Midst of Life: Music from the Baldwin Partbooks I | Byrd, Tallis, Taverner, Sheppard; Contrapunctus, Owen Rees | | 1 |
| 2017 | Virgin and Child - Music from the Baldwin Partbooks II | Taverner, Fayrfax, Tallis, Sheppard; Contrapunctus, Owen Rees | | 1 |
| 2017 | Media vita | John Sheppard; Westminster Cathedral Choir, Martin Baker | | 2 |
| 2020 | Media vita | John Sheppard; Robert Quinney, Choir of New College Oxford | | 2 |
| 2023 | Missa Cantate | John Sheppard; The Tallis Scholars, Peter Phillips | | 2 |
