| 1977 | Poulenc: Mass in G major / Exultate Deo / Salve Regina / Peeters: Missa Festiva op. 62 | Poulenc, Peeters; Choir of St. John’s College, Cambridge, Jonathon Bond, John Scott, George Guest | | 1 |
| 1978 | Mariazeller Mass / Little Organ Mass | Haydn; Jennifer Smith, Helen Watts, Robert Tear, Benjamin Luxon, Choir of St. John’s College, Cambridge, John Scott, Academy of St. Martin-in-the-Fields, George Guest | | 1 |
| 1987 | Organ Music | Marcel Dupré; John Scott | | 1 |
| 1988 | My Soul Doth Magnify the Lord | The Choir of St Paul's Cathedral, John Scott, Christopher Dearnley | | 1 |
| 1988 | My Spirit Hath Rejoiced | St Paul’s Cathedral Choir, John Scott, Christopher Dearnley | | 2 |
| 1989 | Choral Music | Mendelssohn; Corydon Singers, Anne Dawson, John Scott, English Chamber Orchestra, Matthew Best | | 2 |
| 1989 | Favourite Organ Works | John Scott | | 1 |
| 1989 | Praise to the Lord: Favourite Hymns from St Paul’s Cathedral | St Paul’s Cathedral Choir, English Brass Ensemble, Christopher Dearnley, John Scott | | 2 |
| 1990 | The Complete Organ Music of Maurice Duruflé | Maurice Duruflé; John Scott | | 2 |
| 1990 | Hear My Prayer | Jeremy Budd, St Paul’s Cathedral Choir, John Scott | | 1 |
| 1992 | The English Anthem, Volume 2 | The Choir of St Paul’s Cathedral, Andrew Lucas, John Scott | | 1 |
| 1992 | Cathedral Music | Kenneth Leighton; St Paul’s Cathedral Choir, Andrew Lucas, John Scott | | 2 |
| 1994 | The English Anthem, Volume 4 | The Choir of St. Paul's Cathedral, Andrew Lucas, John Scott | | 1 |
| 1994 | Psalms From St Paul's Volume 2: Psalms 18-29 | St Paul's Cathedral Choir, Andrew Lucas, John Scott | | 1 |
| 1995 | Favourite Hymns For All Seasons | The Choir of St. Paul's Cathedral, Barry Rose, John Scott | | 1 |
| 1996 | How Can I Keep From Singing? | St Paul's Cathedral Choristers, City of London Sinfonia, John Scott | | 1 |
| 1997 | Advent at St Paul’s | St Paul’s Cathedral Choir & John Scott | | 1 |
| 1997 | Music for Organ | Mendelssohn; John Scott | | 1 |
| 2002 | Psalms of David - The Complete St Paul's Cathedral Psalter | דָּוִד;John Scott, Andrew Lucas & Huw Tregelles Williams | | 1 |
| 2005 | Christmas on Fifth Avenue | The Choir of Saint Thomas Church, New York City, John Scott | | 1 |
| 2006 | Organ Music by Marcel Dupré | Marcel Dupré; John Scott | | 1 |
| 2008 | Orchestral Works, Volume 1: Organ Concerto / Concerto for String Orchestra / Symphony for Strings | Kenneth Leighton; City of London Sinfonia, Richard Hickox, John Scott | | 1 |
| 2008 | Vespers (All-Night Vigil) | Sergei Rachmaninoff; John Scott, The Saint Thomas Choir of Men and Boys, Ory Brown, David Vanderwal | | 1 |
| 2015 | Dancing Day: Music for Christmas | Saint Thomas Choir of Men and Boys, Fifth Avenue, New York, John Scott | | 1 |
| 2016 | Our Christmas Sequence | St Paul’s Cathedral Choir, Royal Philharmonic Orchestra, John Scott | | 1 |
| 2016 | Requiem, op. 48 | Gabriel Fauré - St. Thomas Choir of Men and Boys, Fifth Avenue, New York, Orchestra of St. Luke’s, John Scott | | 1 |
| 2017 | Requiems | Duruflé, Howells; The Saint Thomas Choir of Men and Boys, John Scott | | 1 |
| — | Twentieth Century Organ Masterpieces | John Scott | | 1 |
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