| 1988 | Cantates | Buxtehude; Schlick, Frimmer, Chance, Jacobs, Pregardien, Kooy, Hannover Knabenchor, The Amsterdam Baroque Orchestra, Ton Koopman | | 1 |
| 1988 | Johannes-Passion | J.S. Bach; H. Crook, P. Lika, B. Schlick, C. Patriasz, W. Kendall, P. Kooy, Collegium Vocale, La Chapelle Royale, Philippe Herreweghe | 4 | 3 |
| 1989 | Messe in H-Moll | J. S. Bach; Chorus and Orchestra of Collegium Vocale, Philippe Herreweghe, Barbara Schlick, Catherine Patriasz, Charles Brett, Howard Crook, Peter Kooy | 5 | 3 |
| 1990 | Magnificat / Cantate BWV 80 | Bach; Schlick, Mellon, Lesne, Crook, Kooy, Collegium Vocale, La Chapelle Royal, Philippe Herreweghe | | 3 |
| 1991 | Cantates pour basse | J.S. Bach; Peter Kooy, La Chapelle Royale, Philippe Herreweghe | 4 | 7 |
| 1991 | Missae BWV 233 & 236 | Johann Sebastian Bach; Agnès Mellon, Gérard Lesne, Christoph Prégardien, Peter Kooy, Chorus and Orchestra of Collegium Vocale, Philippe Herreweghe | | 1 |
| 1992 | Mass in C minor | Mozart; Oelze, Larmore, Weir, Kooy, La Chapelle Royale, Collegium Vocale, Orchestre des Champs‐Élysées, Philippe Herreweghe | | 5 |
| 1993 | Choralpassion, op. 7 | Hugo Distler; Wilfried Jochens, Peter Kooy, Gerrit Miehlke, Kammerchor der Universität Dortmund, Willi Gundlach | | 1 |
| 1993 | St. John Passion | Johann Sebastian Bach; Orchestra of the Eighteenth Century, Annegeer Stumphius, James Bowman, Van der Meel, Christoph Prégardien, Kristinn Sigmundsson, Peter Kooij, Netherlands Chamber Choir, Frans Brüggen | | 1 |
| 1995 | Oster-Oratorium, BWV 249 / Kantate, BWV 66 | J.S. Bach; Barbara Schlick, Kai Wessel, James Taylor, Peter Kooy, Collegium Vocale, Philippe Herreweghe | 3 | 2 |
| 1996 | Weihnachtskantaten, BWV 122, 110, 57 | J.S. Bach; Vasilijka Jezovek, Sarah Connolly, Mark Padmore, Peter Kooy, Collegium Vocale, Philippe Herreweghe | | 2 |
| 1998 | "Mit Freund und Freud", Kantaten 8, 125, 138 | J.S. Bach; Deborah York, Ingeborg Danz, Mark Padmore, Peter Kooy, Collegium Vocale, Philippe Herreweghe | 5 | 3 |
| 1999 | "Wir danken dir, Gott": Cantatas 29, 119 & 120 | J.S. Bach; Deborah York, Ingeborg Danz, Mark Padmore, Peter Kooy, Collegium Vocale, Philippe Herreweghe | | 1 |
| 2000 | Auf dem Wasser zu singen: Water in Songs by Franz Schubert | Franz Schubert; Peter Kooij, Leo van Doeselaar | | 1 |
| 2003 | Cantatas & Masses | J S Bach; Barbara Schlick, Agnès Mellon, Gérard Lesne, Charles Brett, Howard Crook, Christoph Prégardien, Peter Kooy, Collegium Vocale Gent, Philippe Herreweghe | | 1 |
| 2008 | Hercules | Handel; Wemyss, Sämann, Vitzthum, Schoch, Kooij, Kühn, Schneider, Junge Kantorei, Frankfurt Baroque Orchestra, Joachim Carlos Martini | | 1 |
| 2010 | Jesu, meine Freude - Motets | Johann Sebastian Bach; Sette Voci, Peter Kooij | | 1 |
| 2017 | Telemann: Die Stille Nacht | Georg Philipp Telemann, Peter Kooij & L'Armonia Sonora | | 1 |
| 2021 | Christmas Cantatas III | Georg Philipp Telemann; Herfurtner, Günther, Ludwig, Strotmann, Kooij, Die Kölner Akademie, Michael Alexander Willens | | 1 |
| 2021 | Easter Cantatas | Georg Philipp Telemann; Johanna Winkel, Margot Oitzinger, Georg Poplutz, Peter Kooij, Die Kölner Akademie, Michael Alexander Willens | | 1 |
