| 1992 | Great French Virtuosic Organ Music | Jongen, Langlais, Dupré, Bonnet, Demessieux, Widor; Todd Wilson | | 1 |
| 1994 | Jongen: Symphonie Concertante for Organ and Orchestra / Saint‐Saëns: Symphony no. 3 "Organ" | Jongen, Saint‐Saëns; Dallas Symphony Orchestra, Eduardo Mata, Jean Guillou | | 1 |
| 1998 | Danse lente | Joseph Jongen; Marc Grauwels | | 1 |
| 1999 | Symphony no. 3 ‘The Organ’ | Saint‐Saëns, Widor, Grison, Jongen; Jane Parker‐Smith, London Philharmonic Orchestra, Serge Baudo | | 1 |
| 2000 | Works for Organ & Orchestra | Widor, Jongen, Parker; Franz Hauk, The Ingolstadt Philharmonic, Alfredo Ibarra | | 1 |
| 2002 | Flute Sonata / Flute Trio / Danse Lente / Elegy / Two Paraphrases | Joseph Jongen; Marc Grauwels, Marie Hallynck, Sophie Hallynck, Dalia Ouziel, Quatuor de Flûtes du Conservatoire Royal de Bruxelles | | 1 |
| 2002 | In Flanders' Fields Volume. 27: Piano Music | Joseph Jongen, Lodewijk de Vocht, Lodewijk Mortelmans; Hans Ryckelynck | | 1 |
| 2002 | Musique de Chambre Pour Flûte, Harpe et Cordes | Joseph Jongen; Ensemble Arpae | | 1 |
| 2003 | The Complete Organ Works of Joseph Jongen | Joseph Jongen; John Scott Whiteley | | 1 |
| 2006 | Voyage au pays du tendre et de l'effroi | Claude Debussy, Frank Martin, André Caplet, Gabriel Pierné, Joseph Jongen; Oxalys | | 1 |
| 2007 | Complete Organ Works, Volume 1 | Joseph Jongen; Anton Doornhein | | 1 |
| 2007 | Complete Organ Works, Volume 2 | Joseph Jongen; Anton Doornhein | | 1 |
| 2007 | Joseph Jongen: Symphonie Concertante / Camille Saint-Saëns: Symphonie N°3 | Joseph Jongen; Camille Saint‐Saëns; Olivier Latry, Orchestre Philharmonique de Liège, Pascal Rophé | | 1 |
| 2007 | Joseph Jongen: Mass For Choir, Organ And Brass / Flor Peeters: Missa Festiva | Joseph Jongen; Flor Peeters; The Choir Of St. John's College Cambridge, London City Brass, David Hill | | 1 |
| 2011 | Complete Works for Viola and Piano | Joseph Jongen | | 1 |
| 2014 | Harp Concertos | Glière, Jongen, Rodrigo; Anneleen Lenaerts, Brussels Philharmonic, Michel Tabachnik | | 1 |
| 2015 | Jongen: Violin Concerto in B minor, op. 17 / Adagio symphonique in B major, op. 20 / Fantasia in E major, op. 12 / Lazzari: Rapsodie in E minor | Jongen, Lazzari; Philippe Graffin, Royal Flemish Philharmonic, Martyn Brabbins | | 2 |
| 2015 | Pages intimes | Joseph Jongen; Nathan Braude, Orchestre Philharmonique Royal de Liège, Jean-Pierre Haeck | | 1 |
| 2016 | Chamber Music | Joseph Jongen; Oxalys | | 1 |
| 2016 | Symphonie Concertante Op. 81 / Passacaglie Et Gigue Op. 90 / Sonata Eroica Op. 94 | Joseph Jongen; Christian Schmitt, Deutsche Radio Philharmonie Saarbrücken Kaiserslautern, Martin Haselböck | | 1 |
| 2017 | La Musique | Joseph Jongen; Claire Lefilliâtre, Oxalys | | 1 |
| 2017 | Oeuvres Pour Violoncelle Et Orchestre | Joseph Jongen; Henri Demarquette, Orchestre Philharmonique Royal de Liège, Christian Arming | | 1 |
| 2019 | Entrevisions. Intégrale des mélodies, Vol. I | Joseph Jongen; Sarah Defrise, Craig White | | 1 |
| 2023 | 13 Préludes; 24 Petits Préludes dans tous les tons | Joseph Jongen; Ivan Ilić | | 1 |
| 2023 | Fêtes rouges. Intégrale des mélodies, Vol. 2 | Joseph Jongen; Sarah Defrise, Craig White | | 1 |
| — | A Grand Celebration: The Historic Court Concert For Macy's 150th Anniversary | Joseph Jongen | | 1 |
