| 1993 | Sonate en si bémol majeur / Sonate en fa majeur opus 17 / Sérénade en ré opus 41 | Beethoven; Emmanuel Pahud, Eric Lesage | | 2 |
| 1997 | Flöten Konzerte 1 & 2 / Konzert für Flöte und Harfe | Mozart; Emmanuel Pahud, Marie‐Pierre Langlamet, Berliner Philharmoniker, Claudio Abbado | | 1 |
| 1998 | Paris | Poulenc, Dutilleux, Sancan, Ibert, Milhaud, Messiaen, Jolivet; Emmanuel Pahud, Éric Le Sage | | 1 |
| 1998 | Cantos y danzas | Brouwer, Mangoré, Ponce, Villa‐Lobos, Gnattali, Grenet, Lauro, Piazzolla; Manuel Barrueco, Barbara Hendricks, Emmanuel Pahud | | 1 |
| 1999 | Quatuors avec flute | Mozart; Emmanuel Pahud | | 2 |
| 2000 | Tico-Tico: Best Loved Brazilian Melodies | Daniel Barenboim, Emmanuel Pahud | | 2 |
| 2000 | Debussy: Syrinx / Bilitis / La plus que lente / Ravel: Chansons madécasses / Prokofiev: Flute Sonata | Claude Debussy, Maurice Ravel, Sergei Prokofiev; Emmanuel Pahud, Stephen Kovacevich | | 1 |
| 2001 | The Canticle of the Sun / Music for Flute, Strings and Percussion | Sofia Gubaidulina; Emmanuel Pahud, Mstislav Rostropovich | | 1 |
| 2001 | Johann Sebastian Bach, Brandenburg Concerto No. 5, Etc. | Emmanuel Pahud, Berliner Barock Solisten, Rainer Kussmaul, Christine Schornsheim & Georg Faust | | 1 |
| 2002 | Flute Concertos | Telemann; Emmanuel Pahud, Berliner Barock Solisten, Rainer Kussmaul | | 1 |
| 2003 | Into the Blue | Emmanuel Pahud & Jacky Terrasson | | 1 |
| 2003 | Flute Concertos | Ibert, Khachaturian; Emmanuel Pahud, Tonhalle‐Orchester Zürich, David Zinman | | 2 |
| 2004 | Works for Flute | César Franck, Charles‐Marie Widor, Richard Strauss; Emmanuel Pahud, Éric Le Sage | | 1 |
| 2005 | French Connection | Emmanuel Pahud, Éric Le Sage, Paul Meyer | | 1 |
| 2006 | Flute Concertos | Vivaldi; Australian Chamber Orchestra, Richard Tognetti, Emmanuel Pahud | | 1 |
| 2007 | Clarinet & Flute Concertos / Wind Quintet | Nielsen; Sabine Meyer, Emmanuel Pahud, Berliner Philharmoniker, Simon Rattle | | 1 |
| 2007 | ... Prisme / Incidences ... | Michael Jarrell; Emmanuel Pahud, Paul Meyer, François Leleux, Hae-Sun Kang, Marino Formenti, Orchestre de la Suisse Romande, Pascal Rophé | | 1 |
| 2008 | Flute Concertos | Dalbavie, Jarrell, Pintscher; Emmanuel Pahud | | 1 |
| 2008 | Complete Flute Sonatas | Johann Sebastian Bach; Emmanuel Pahud, Trevor Pinnock | | 2 |
| 2012 | Flute Concertos & Scherzandi | F. J. & J. M. Haydn; Haydn‐Ensemble Berlin, Hansjörg Schellenberger, Emmanuel Pahud | | 2 |
| 2013 | The Flute King: Music From the Court of Frederick the Great | Emmanuel Pahud | | 1 |
| 2013 | Dolly / 4 mains / Masques et bergamasques / Fantaisie, op. 79 / Trio, op. 120 | Gabriel Fauré; Le Sage, Tharaud, Pahud, Colombet, Merlin | | 2 |
| 2013 | Around the World | Emmanuel Pahud, Christian Rivet | | 1 |
| 2015 | Revolution | Devienne, Gianella, Gluck, Pleyel; Emmanuel Pahud, Kammerorchester Basel, Giovanni Antonini | | 3 |
| 2016 | Flute Concertos | CPE Bach; Emmanuel Pahud, Kammerakademie Potsdam, Trevor Pinnock | | 3 |
| 2017 | Sonates & Trio | Debussy; Renaud Capuçon, Bertrand Chamayou, Gérard Caussé, Emmanuel Pahud, Marie‐Pierre Langlamet, Edgar Moreau | | 1 |
| 2018 | Solo | Emmanuel Pahud | | 1 |
| 2019 | Doppler Discoveries | Franz Doppler, Carl Doppler; András Adorján & Emmanuel Pahud, Jan Philip Schulze, Arcis Hornquartett | | 1 |
| 2019 | Works For Harp | Nino Rota; Anneleen Lenaerts, Emmanuel Pahud, Brussels Philharmonic, Adrien Perruchon | | 1 |
| 2019 | Dreamtime | Emmanuel Pahud, Münchner Rundfunkorchester, Ivan Repušić | | 2 |
| 2020 | Vienne 1900 | Emmanuel Pahud, Paul Meyer, Daishin Kashimoto, Zvi Plesser, Éric Le Sage | | 2 |
| 2020 | Airlines | Alexandre Desplat; Orchestre national de France, Emmanuel Pahud | | 3 |
| 2020 | Beethoven | Beethoven; Emmanuel Pahud, Daniel Barenboim, Daishin Kashimoto, Amihai Grosz, Silvia Careddu, Sophie Dervaux | | 2 |
| 2021 | Chamber Music | Nino Rota; Emmanuel Pahud, Paul Meyer, Éric Le Sage, Daishin Kashimoto, Joaquín Riguelme García, Aurélien Pascal, Claudio Bohórquez, Olivier Thiery, François Meyer, Gilbert Audin, Benoît de Barsony | | 2 |
| 2021 | Æther | Sarah Aristidou, Daniel Barenboim, Emmanuel Pahud, Christian Rivet, Orchester des Wandels, Thomas Guggeis | | 1 |
| 2021 | Mozart & Flute in Paris | Mozart; Emmanuel Pahud, Lenaerts, Audin, Leleux, Meyer, Vlatković, Orchestre de chambre de Paris, François Leleux | | 1 |
| 2023 | Romances | Emmanuel Pahud & Eric Le Sage | | 1 |
| 2024 | Mozart Stories | Wolfgang Amadeus Mozart; Emmanuel Pahud & Eric Le Sage | | 1 |
