| 1975 | Concertos & Suites | Muffat; La Petite Bande | | 2 |
| 1982 | Armonico tributo: Salzburg 1682 | Georg Muffat; The Parley of Instruments, Roy Goodman, Peter Holman | | 3 |
| 1987 | Florilegium Secundum, Fasciculi I-IV | Georg Muffat; Academy of Ancient Music, Christopher Hogwood | | 2 |
| 1989 | Orgues De France - Malaucène | Georg Muffat; René Saorgin | | 1 |
| 1989 | Orgues Historiques / France | Georg Muffat; René Saorgin | | 1 |
| 1990 | Apparatus Musico-Organisticus | Georg Muffat; Jaroslav Tůma | | 2 |
| 1990 | German Harpsichord Music Before Bach | Kerll, Froberger, Pachelbel, Buxtehude, Weckmann, Muffat; Jacques Ogg | | 1 |
| 1992 | Schnitgerorgel der AA-kerk Groningen / Christiaan Teeuwsen | Georg Böhm, Johann Gottfried Walther, Dietrich Buxtehude, Heinrich Scheidemann, Georg Muffat & Vincent Lübeck | | 1 |
| 1994 | Apparatus musico-organisticus 1690 | Georg Muffat; Elisabeth Ullmann | | 1 |
| 1996 | Armonico Tributo | Muffat; Ensemble 415, Chiara Banchini, Jesper Christensen | | 1 |
| 1997 | Spirit of the Baroque | Purcell, Avison, Muffat, Geminiani; Tasmanian Symphony Chamber Players, Geoffrey Lancaster | | 1 |
| 1999 | Muffat: Suite Indissolubilis Amicitia / Concerto Bona nova / Biber: Sonata a 6 "called Peasants' Church-going" / Sonata a 2 violini, trombone, violone / Sonata VIII / Battalia a 10 | Georg Muffat, Heinrich Ignaz Franz von Biber; Concentus Musicus Wien, Nikolaus Harnoncourt | | 1 |
| 2000 | Organ Works, Volume 1: Apparatus musico-organisticus, part I | Georg Muffat; Martin Haselböck | | 1 |
| 2000 | Organ Works, Volume 2: Apparatus musico-organisticus, part II | Georg Muffat; Martin Haselböck | | 1 |
| 2001 | Armonico Tributo, 1682 | Georg Muffat; Ars Antiqua Austria, Gunar Letzbor | | 1 |
| 2004 | Der Türken Anmarsch | Biber, Muffat; John Holloway | | 1 |
| 2004 | Complete Clavier Works | Georg Muffat; Siegbert Rampe | | 1 |
| 2005 | Apparatus musico-organisticus | Georg Muffat; Joseph Kelemen | | 1 |
| 2005 | Armonico tributo | Georg Muffat; Les Muffatti, Peter Van Heyghen | | 1 |
| 2008 | Concertos I - VII | Georg Muffat; Holland Baroque Society, Matthew Halls | | 1 |
| 2013 | Complete Apparatus Musico-Organisticus | Muffat; Adriano Falcioni | | 2 |
| 2016 | Missa In Labore Requies | Georg Muffat, Antonio Bertali, Heinrich Ignaz Franz Biber von Bibern, Johann Heinrich Schmelzer;Cappella Murensis & Les Cornets Noirs | | 1 |
| 2018 | The Versailles Revolution | Jean‐Baptiste Lully, Georg Muffat, Marin Marais; Indianapolis Baroque Orchestra, Barthold Kuijken | | 2 |
| 2022 | The Habsburg Garden of Eden | Caldara, Bonporti, Handel, Biber, Ziani, Muffat; Ensemble Arava | | 1 |
| 2023 | Armonico Tributo | Georg Muffat; Concerto Copenhagen, Lars Ulrik Mortensen | | 1 |
| — | Grote Kerk Zwolle | Buxtehude, Böhm, Scheidemann, Georg Muffat, J.S. Bach, C.P.E Bach; Wouter van den Broek | | 1 |
| — | Propitia Sydera | Georg Muffat | | 1 |
| — | Spielereien: The Baroque Organist's Playthings | Bach, Couperin, Dandrieu, Kerll, Martini, Muffat, Scheidt; Franz Haselböck | | 1 |
| — | Sonatas | Freiburger Barockorchester Consort;Heinrich Ignaz Franz von Biber;Georg Muffat | | 1 |
