| 1991 | The Sacred Trombone | Read, Liszt, Hillborg, Eben, Schnittke, Sandström; Christian Lindberg, Gunnar Idenstam | | 1 |
| 1993 | 20th Century Music for Trumpet and Organ | Eben, Plog, Hovhannes, Persichetti, Jolivet, Douglas Lowry; Anthony Plog, Hans-Ola Ericsson | | 1 |
| 1995 | Three Old Testament Frescoes | Eben, Korte, Kalabis | | 1 |
| 1995 | Dvořák: Moravian Duets, op. 32 / Suk: Ten Songs / Smetana: Three Choruses / Eben: About Swallows and Girls | Dvořák, Suk, Smetana, Eben; Prague Chamber Choir, Josef Pančík | | 1 |
| 1996 | Dvořák / Janáček / Eben | Dvořák, Janáček, Eben; Prague Chamber Choir, Josef Pančík | | 2 |
| 1997 | Great European Organs, No. 51: Peter King Plays the Klais Organ of Bath Abbey | Buxtehude, Böhm, Liszt, Guridi, Bach, Saint‐Saëns, Eben; Peter King | | 1 |
| 2000 | The Organ Music of Petr Eben 1: Job / Laudes / Hommage à Buxtehude | Petr Eben; Halgeir Schiager | | 1 |
| 2001 | The Organ Music of Petr Eben 2: Faust / Four Biblical Dances | Petr Eben; Halgeir Schiager | | 1 |
| 2001 | Hammered Brass | Luciano Berio, Robert Crawford, Petr Eben, Steve Martland, Iannis Xenakis; The Wallace Collection | | 1 |
| 2002 | The Organ Music of Petr Eben 3: Mutationes / Ten Chorale Preludes | Petr Eben; Halgeir Schiager | | 1 |
| 2002 | Das Orgelwerk Vol. 1 | Petr Eben; Gunther Rost | | 1 |
| 2002 | Das Orgelwerk Vol. 2: Hiob | Petr Eben; Gunther Rost, Gert Westphal | | 1 |
| 2005 | The Organ Music of Petr Eben 4: Protestant Chorales / Sunday Music | Petr Eben; Halgeir Schiager | | 1 |
| 2005 | Das Orgelwerk Vol. 3 | Petr Eben; Gunther Rost | | 1 |
| 2006 | The Organ Music of Petr Eben 5: Landscapes of Patmos / Okna | Petr Eben; Halgeir Schiager | | 1 |
| 2006 | Das Orgelwerk Vol. 4 | Petr Eben; Gunther Rost | | 1 |
| 2006 | Das Orgelwerk Vol. 5 | Petr Eben; Gunther Rost, Gert Westphal | | 1 |
| 2009 | Risonanza | Hanuš, Eben, Pavel Haas; Kateřina Englichová, Vilém Veverka, Ivo Kahánek | | 1 |
| 2009 | Zwiesprache | Petr Eben | | 1 |
| 2010 | Piano Trios | Eben, Martinů, Smetana; The Florestan Trio | | 1 |
| 2010 | Symphonia Gregoriana | Petr Eben; Gunther Rost, Bamberger Symphoniker, Gabriel Feltz | | 1 |
| 2012 | Landscapes of Patmos / Okna / Concerto no. 2 for Organ | Petr Eben; Gunther Rost, Tine Thing Helseth, Babette Haag, Bamberger Symphoniker, Gabriel Feltz | | 1 |
| 2017 | String Quartet “Labyrinth of the World and Paradise of the Heart”, Piano Trio and Piano Quintet | Petr Eben; Karel Košárek & Martinů Quartet | | 1 |
| 2019 | Twentieth Century Oboe Sonatas | Bowen, Eben, Dutilleux, Bozza, Poulenc, Saint‐Saëns; Alex Klein, Phillip Bush | | 2 |
| — | Произведения для органа | Бах, Лист, Карг-Элерт, Шёнберг, Эбен; Даниил Процюк | | 1 |
