| 1958 | Pièce héroïque / Three Chorales | Franck; Marcel Dupré | | 3 |
| 1960 | Dupré at Saint-Sulpice, Vol. 4: Bach | Bach; Marcel Dupré | | 3 |
| 1961 | Organ Music From France | Virgil Fox, Maurice Duruflé, Louis Vierne, César Franck, Marcel Dupré | | 1 |
| 1973 | Michael Murray Playing the Organ at Grace Cathedral, San Francisco | Lemmens, Vierne, Dupré, Widor; Michael Murray | | 1 |
| 1978 | Le Chemin de la Croix | Marcel Dupré; Suzanne Chaisemartin | | 1 |
| 1986 | Dupré: Symphony in G minor / Rheinberger: Organ Concerto no. 1 in F | Dupré, Rheinberger; Royal Philharmonic Orchestra, Jahja Ling, Michael Murray | | 1 |
| 1986 | Orgelwerke | Marcel Dupré; Daniel Roth | | 1 |
| 1986 | Pierre Cochereau aux grandes orgues de Notre-Dame de Paris | Marcel Dupré; Pierre Cochereau | | 2 |
| 1986 | Welte-Philharmonie-Orgel | Max Reger, Eugène Gigout, Joseph Bonnet, Marcel Dupré | | 1 |
| 1987 | Organ Music | Marcel Dupré; John Scott | | 1 |
| 1988 | Great European Organs, No. 7: Jane Watts Plays the Organ of Westminster Abbey | Guilmant, Karg‐Elert, Dupré; Jane Watts | | 2 |
| 1988 | Great European Organs, No. 8: Graham Barber Plays the Klais Organ of Ingolstadt Minster | Dupré, Demessieux; Graham Barber | | 2 |
| 1989 | Great European Organs, No. 16: David Briggs Plays the Henry Willis Organ of St George’s Hall, Liverpool | Vierne, Dupre, Cochereau; David Briggs | | 2 |
| 1991 | Les Symphonies pour orgue | Marcel Dupré; Suzanne Chaisemartin | | 1 |
| 1991 | Organ Music | Marcel Dupré; Jeremy Filsell | | 1 |
| 1992 | Great French Virtuosic Organ Music | Jongen, Langlais, Dupré, Bonnet, Demessieux, Widor; Todd Wilson | | 1 |
| 1992 | Widor: Allegro (from Symphony no. 6) / Salve Regina / Franck: Pièce héroïque / Three Chorales | Widor, Franck; Marcel Dupré | | 1 |
| 1993 | Organ Music of César Franck and Marcel Dupré | César Franck, Marcel Dupré; David Schrader | | 1 |
| 1993 | Symphonies pour orgue | Marcel Dupré; Yves Castagnet | | 1 |
| 1994 | Dupré: Konzert in e-Moll, op. 31 / Demessieux: Poème, op. 9 / Dupré: Orgelwerke | Marcel Dupré, Jeanne Demessieux; Symphonisches Orchester Zürich, Daniel Schweizer, Ulrich Meldau | | 1 |
| 1994 | Französische Orgelsymphonik des 19. & 20. Jahrhunderts | Vierne, Franck, Dupré, Litaize, Escaich; Denis Comtet | | 1 |
| 1994 | Orgelwerke | Marcel Dupré; Klaus Rothaupt | | 1 |
| 1995 | Hans Fagius plays French Organ Music | Couperin, Alain, Duruflé, Saint‐Saëns, Boëllmann, d'Aquin, Dupré; Hans Fagius | | 1 |
| 1995 | Poulenc, Dupré, Messiaen, Bonnet | Poulenc, Dupré, Messiaen, Bonnet; Kalevi Kiviniemi, Moscow Chamber Orchestra, Constantine Orbelian | | 1 |
| 1997 | Vierne: Messe solennelle / Widor: Messe à deux chœurs et deux orgues / Dupré: Quatre Motets | Vierne, Widor, Dupré; Westminster Cathedral Choir, James O’Donnell | | 1 |
| 1997 | Les Orgues de la collégiale de Neuchâtel | Norbert Moret, Marcel Dupré, Guy Bovet; Marcel Dupré, Guy Bovet | | 2 |
| 1998 | Works for Organ, Volume 3 | Marcel Dupré; Columbus Indiana Philharmonic, David Bowden, Daniel Jay McKinley | | 1 |
| 1999 | Works for Organ, Volume 7 | Marcel Dupré; Mary Preston | | 1 |
| 1999 | Works for Organ, Vol. 9 | Marcel Dupré; Bruce Neswick, Timothy Durbin, Jennifer Rende, Clyde Beavers | | 1 |
| 1999 | Organ Works, Volume 1 | Marcel Dupré; Ben van Oosten | | 1 |
| 1999 | Works for Organ Vol. 8 | Marcel Dupré | | 1 |
| 2000 | Works for Organ, Volume 11: The Way of the Cross | Marcel Dupré; Mary Preston | | 1 |
| 2000 | Great European Organs, No. 64: Daniel Roth Plays the Great Organ of Saint-Sulpice, Paris | Nivers, Clérambault, Séjan, Schmitt, Lefébure‐Wély, Widor, Grunenwald, Roth, Dupré | | 1 |
| 2001 | Organ Works, Volume 2 | Marcel Dupré; Ben van Oosten | | 1 |
| 2002 | Organ Works, Volume 3 | Marcel Dupré; Ben van Oosten | | 1 |
| 2002 | Organ Works, Volume 4 | Marcel Dupré; Ben van Oosten | | 1 |
| 2003 | Organ Works, Volume 5 | Marcel Dupré; Ben van Oosten | | 1 |
| 2004 | Louis Robilliard plays Dupré, Fauré & Duruflé | Dupré, Fauré, Duruflé; Louis Robilliard | | 1 |
| 2004 | Organ Works, Volume 6 | Marcel Dupré; Ben van Oosten | | 1 |
| 2005 | King of Instruments: The Art of Gillian Weir, Vol. 5 | Camilleri, Widor, Vierne, Daquin, Dupré, Tomkins, Sweelinck, Dubois; Gillian Weir | | 1 |
| 2005 | Le Chemin de la Croix / Gregorian Chants | Marcel Dupré; Friedhelm Flamme, Gregorianik-Schola Marienmünster Corvey | | 1 |
| 2005 | Organ Works, Volume 7 | Marcel Dupré; Ben van Oosten | | 1 |
| 2006 | Organ Music by Marcel Dupré | Marcel Dupré; John Scott | | 1 |
| 2007 | Organ Works, Volume 8 | Marcel Dupré; Ben van Oosten | | 1 |
| 2008 | Organ Works, Volume 9 | Marcel Dupré; Ben van Oosten | | 1 |
| 2008 | Organ Works, Volume 10 | Marcel Dupré; Ben van Oosten | | 1 |
| 2010 | Organ Works, Volume 11 | Marcel Dupré; Ben van Oosten | | 1 |
| 2010 | Organ Works, Volume 12 | Marcel Dupré; Ben van Oosten | | 1 |
| 2010 | Trilogies | Marcel Dupré, Jehan Alain; Gunther Rost | | 1 |
| 2014 | Dupré: Passion Symphony, op. 23 / Vierne: Symphony no. 3, op. 28 | Marcel Dupré, Louis Vierne; J. Thomas Mitts | | 1 |
| 2014 | Salve Regina | Bourdon, Carol, Dupré, Falcinelli, Hakim, Peeters, Tournemire; Olivier Vernet | | 1 |
| 2015 | The Mercury Living Presence Recordings | Marcel Dupré | | 1 |
| 2015 | Dupré at Saint-Sulpice, Vol. 2: The music of Marcel Dupré | Marcel Dupré | | 2 |
| 2015 | Dupré at Saint-Sulpice, Volume Three: Franck | Franck; Marcel Dupré | | 2 |
| 2015 | Marcel Dupré at Saint-Sulpice, Vol. 1: Bach | Bach; Marcel Dupré | | 2 |
| 2015 | Marcel Dupré at Saint-Sulpice, Vol. 5: Dupré and Messiaen | Dupré, Messiaen; Marcel Dupré | | 2 |
| 2015 | Organ Recital: Music by Widor and Dupré | Dupré, Widor; Marcel Dupré | | 2 |
| 2015 | Symphony no. 3 in C minor, op. 78 | Camille Saint‐Saëns; Marcel Dupré, Paul Paray, Detroit Symphony Orchestra | | 2 |
| 2017 | Jean-Willy Kunz au grand orgue Pierre-Béique | Saint‐Saëns, Bach, Goulet, Dupré, Alain, Vierne; Jean-Willy Kunz | | 1 |
| 2020 | Passion Symphony | Dupré; Wayne Marshall | | 1 |
| 2022 | Romantic Music for Cello and Organ | Wermann, Rheinberger, Brahms, Widor, Shmitov, Dupré; Alexander Zagorinsky, Alexey Shmitov | | 1 |
| 2022 | Saint-Saens Symphony No. 3 - Dupre - Paray | Marcel Dupré, Paul Paray & Detroit Symphony Orchestra | | 1 |
| — | Die Orgel im Dom zu Trier | Rheinberger, Karg-Elert, Fackler, Dupré, Messiaen, Guilmant; Wolfgang Oehms | | 1 |
| — | Französische Chormusik mit zwei Orgeln | Charles‐Marie Widor, Erik Satie, Eugène Gigout, Francis Poulenc, Marcel Dupré; Elisabeth Sperer, Winfried Englhardt, Münchner Madrigalchor, Franz Brandl | | 1 |
