| 1990 | Das Orgelwerk / L'Oeuvre d'Orgue / The Organ Works Vol. I | Jehan Alain; Helga Schauerte-Maubouet | | 1 |
| 1991 | Oeuvres Instrumentales & Vocales | Jehan Alain; Georges Guillard | | 1 |
| 1993 | Piet Kee at the Concertgebouw | Alain, Franck, Saint‐Saëns; Piet Kee | | 2 |
| 1995 | Hans Fagius plays French Organ Music | Couperin, Alain, Duruflé, Saint‐Saëns, Boëllmann, d'Aquin, Dupré; Hans Fagius | | 1 |
| 1995 | Œuvres Instrumentales & Vocales Vol.2 | Jehan Alain; Georges Guillard | | 1 |
| 1998 | The Complete Works for Organ | Jehan Alain; Kevin Bowyer | | 1 |
| 1999 | Œuvres Instrumentales & Vocales Vol.3 | Jehan Alain; Georges Guillard | | 1 |
| 2000 | Complete Works for Organ, Volume 1 | Jehan Alain; Marie‐Claire Alain | | 1 |
| 2001 | Complete Works for Organ, Volume 2 | Jehan Alain; Marie‐Claire Alain | | 1 |
| 2002 | Französische Orgelmusik in der Abtei Marienstatt | Couperin, Widor, Alain, Messiaen; Elisabeth Wangelin-Buschmann | | 1 |
| 2004 | Das Orgelwerk / L'Oeuvre d'Orgue / The Organ Works Vol. II | Jehan Alain; Helga Schauerte-Maubouet | | 1 |
| 2005 | Poulenc: Organ Concerto / Alain, Duruflé: Organ Works | Poulenc, Duruflé, Alain; Marie‐Claire Alain, Bamberger Symphoniker, Jean-Jacques Kantorow | | 2 |
| 2010 | Trilogies | Marcel Dupré, Jehan Alain; Gunther Rost | | 1 |
| 2015 | Solitaires | Ravel, Messiaen, Alain, Dutilleux; Kathryn Stott | | 1 |
| 2016 | Poulenc: Concerto for Organ / Alain: Suite for Organ | Poulenc, Alain; Kjell Johnsen | | 1 |
| 2017 | Jean-Willy Kunz au grand orgue Pierre-Béique | Saint‐Saëns, Bach, Goulet, Dupré, Alain, Vierne; Jean-Willy Kunz | | 1 |
| 2018 | Visages impressionnistes | Fauré, Debussy, Florentz, Alain, Robin; Louis-Noël Bestion de Camboulas | | 1 |
| — | L'Œuvre pour orgue, vol. 1 | Jehan Alain; Marie‐Claire Alain | | 1 |
| — | L'Œuvre pour orgue, vol. 2 | Jehan Alain; Marie‐Claire Alain | | 1 |
| — | Marie-Claire Alain joue Jehan Alain | Jehan Alain; Marie‐Claire Alain | | 2 |
| — | Organ Works | Jehan Alain; Thomas Trotter | | 1 |
