| 1996 | Piano Quintet / Songs of a Winter Night / 13 Slovak Songs | Vítězslav Novák; Radoslav Kvapil, Kocian Quartet, Magdalena Kožená | | 1 |
| 1997 | Bach Arias | Magdalena Kožená | | 2 |
| 1999 | Dixit Dominus | Händel; Les Musiciens du Louvre, Marc Minkowski, Annick Massis, Magdalena Kožená | | 1 |
| 1999 | Pastorely, Česká mše vánoční | Jakub Jan Ryba; Magdalena Kožená, Capella Regia Musicalis, Robert Hugo, Gabriela Eibenová, Jaroslav Březina & Michael Pospíšil | | 1 |
| 2000 | Love Songs | Dvořák, Janáček, Martinů; Magdalena Kožená, Graham Johnson | | 1 |
| 2000 | Italian Cantatas | Georg Friedrich Händel; Magdalena Kožená, Les Musiciens du Louvre, Marc Minkowski | | 2 |
| 2001 | Juditha triumphans | Vivaldi; Magdalena Kožená, Academia Montis Regalis, Alessandro De Marchi | | 2 |
| 2002 | Le belle immagini | Mozart, Gluck, Mysliveček; Magdalena Kožená | | 1 |
| 2003 | French Arias | Magdalena Kožená, Mahler Chamber Orchestra & Marc Minkowski | | 1 |
| 2004 | Songs | Magdalena Kožená | | 1 |
| 2005 | Lamento | Magdalena Kožená, Musica Antiqua Köln, Reinhard Goebel | 5 | 2 |
| 2006 | Arias | Mozart; Magdalena Kožená, Orchestra of the Age of Enlightenment, Simon Rattle | 2 | 2 |
| 2006 | La clemenza di Tito | Mozart; Magdalena Kožená, Rainer Trost, Hillevi Martinpelto, Scottish Chamber Orchestra, Sir Charles Mackerras | | 1 |
| 2007 | Ah! mio cor: Handel Arias | George Frideric Handel; Magdalena Kožená, Venice Baroque Orchestra, Andrea Marcon | 3 | 1 |
| 2007 | Juditha Triumphans | Vivaldi; Magdalena Kožená, Academia Montis Regalis, Alessandro De Marchi | | 2 |
| 2008 | Songs My Mother Taught Me | Magdalena Kožená & Malcolm Martineau | | 1 |
| 2009 | Three fragments from the opera Juliette | Bohuslav Martinů, Charles Mackerras, Česká filharmonie, Magdalena Kožená, Steve Davislim | | 1 |
| 2009 | Vivaldi | Vivaldi; Magdalena Kožená, Venice Baroque Orchestra, Andrea Marcon | | 1 |
| 2009 | Czech Christmas Mass | Jakub Jan Ryba; Magdalena Kožená, Capella Regia Musicalis, Robert Hugo | | 1 |
| 2010 | Des Knaben Wunderhorn / Adagio From Symphony no. 10 | Mahler; Kožená, Gerhaher, The Cleveland Orchestra, Pierre Boulez | | 1 |
| 2010 | Lettere Amorose | Magdalena Kožená, Private Musicke & Pierre Pitzl | | 1 |
| 2010 | Festliches Adventskonzert aus der Dresdner Frauenkirche | Gabetta, Hampson, Kožená | | 1 |
| 2010 | Symphony No. 4 / Rückert-Lieder | Mahler; Magdalena Kožená, Claudio Abbado, Lucerne Festival Orchestra | | 1 |
| 2010 | Magdalena Kožená singt Bach | Magdalena Kožená | | 1 |
| 2012 | Love and Longing | Dvořák, Ravel, Mahler; Magdalena Kožená, Berliner Philharmoniker, Simon Rattle | | 2 |
| 2012 | Bach - Bachianas (Music by the Bach family) | Johann Sebastian Bach; Magdalena Kožená, Musica Antiqua Köln, Reinhard Goebel | | 1 |
| 2012 | Carmen | Georges Bizet; Magdalena Kožená, Jonas Kaufmann, Genia Kühmeier, Kostas Smoriginas, Berliner Philharmoniker, Simon Rattle | | 2 |
| 2013 | Handel: Messiah | Handel; Lynne Dawson, Magdalena Kožená, Brian Asawa, John Mark Ainsley, Les Musiciens du Louvre, Marc Minkowski | | 1 |
| 2015 | Giulio Cesare / Ariodante / Hercules | George Frideric Handel; Anne Sofie von Otter, Marijana Mijanovic, Magdalena Kožená, Lynne Dawson, Gidon Saks, Les Musiciens du Louvre, Marc Minkowski | | 1 |
| 2016 | Monteverdi | Claudio Monteverdi; Magdalena Kožená, La Cetra, Andrea Marcon | | 2 |
| 2017 | La Mer / Ariettes Oubliées / Pelléas Et Mélisande | Debussy, Fauré; Magdalena Kožená, Deutsches Symphonie-Orchester Berlin, Robin Ticciati | | 1 |
| 2018 | Das Lied von der Erde | Gustav Mahler; Magdalena Kožená, Stuart Skelton, Symphonieorchester des Bayerischen Rundfunks, Simon Rattle | | 1 |
| 2018 | Aimer et mourir – Danses et mélodies | Ravel, Duparc; Robin Ticciati, Magdalena Kožená, Deutsches Symphonie‐Orchester Berlin | | 2 |
| 2019 | Soirée | Magdalena Kožená & Friends | | 1 |
| 2019 | Debussy: Nocturnes / Duruflé: Requiem | Debussy, Duruflé; Robin Ticciati, Magdalena Kožená, Deutsches Symphonie-Orchester Berlin, Rundfunkchor Berlin | | 1 |
| 2021 | Nostalgia | Magdalena Kožená, Yefim Bronfman | | 2 |
| 2023 | Folk Songs | Magdalena Kožená, Czech Philharmonic, Sir Simon Rattle | | 2 |
| 2024 | Alcina | Handel; Magdalena Kožená, Erin Morley, Anna Bonitatibus, Elizabeth DeShong, Les Musiciens du Louvre, Marc Minkowski | | 2 |
| 2024 | Czech Songs | Magdalena Kožená, Czech Philharmonic, Sir Simon Rattle | | 1 |
