| 1962 | Mannheim And Vienna (XII. Research Period – Series C: From The 'Galant' To The 'Biedermeier') | Leopold Mozart, Michael Haydn & Johann Christian Bach | | 1 |
| 1981 | Mozart: Duos for Violin and Viola K. 423 & 424 / Haydn: Duo No.1 for Violin and Viola | Mozart, Michael Haydn; Mark Lubotsky, Nobuko Imai | | 1 |
| 1983 | Deutsche Messen | Franz Schubert / Michael Haydn / Rainer van Husen / Michael Flöth / Bläserensemble Münster / Der Domchor Münster / Heinz-Gert Freimuth | | 1 |
| 1985 | Symphonies No. 19 in C, No. 23 in D, No. 26 in G | Michael Haydn; Bournemouth Sinfonietta, Harold Farberman | | 1 |
| 1986 | Symphonies | Michael Haydn; Bournemouth Sinfonietta, Harold Farberman | | 1 |
| 1986 | Six Trumpet Concertos | J. Haydn, G. Torelli, M. Haydn, G. P. Telemann, J. B. Neruda, J. Humphries; Crispian Steele‐Perkins, English Chamber Orchestra, Anthony Halstead | | 1 |
| 1988 | Streichquartette (Sonare Quartett) | Michael Haydn | | 1 |
| 1989 | Missa Sancti Francisci, Requiem | Michael Haydn; Hungarian Radio and Television Chorus, Liszt Ferenc Chamber Orchestra Budapest & Helmuth Rilling | | 1 |
| 1990 | Trumpet Concertos | M. Haydn, Hertel, Molter, L. Mozart, Richter; Håkan Hardenberger, London Philharmonic Orchestra, Elgar Howarth | | 1 |
| 1993 | Flötenkonzerte / Sinfonie F-Dur | Michael Haydn; István-Zsolt Nagy, Österreichisch‐Ungarische Haydn‐Philharmonie, Ádám Fischer | | 1 |
| 1993 | Mozart: Horn Quintet / Beethoven: Sextet / Reicha: Quintet / J. Haydn: Trio / M. Haydn: Romance | Mozart, Beethoven, Reicha, J. Haydn, M. Haydn; Hermann Baumann, Gewandhaus-Quartett | | 1 |
| 1993 | Symphonies 1-3 | Michael Haydn; Slovenský komorný orchester Bohdana Warchala, Bohdan Warchal | | 1 |
| 1994 | String Quintets: B-flat major / C major / G major | Michael Haydn; L'Archibudelli | | 1 |
| 1996 | Symphonies | Michael Haydn; London Mozart Players, Matthias Bamert | | 1 |
| 1997 | Trombone Concerti | Albrechtsberger, Wagenseil, Leopold Mozart, Michael Haydn; Northern Sinfonia, Alain Trudel | | 1 |
| 1997 | Joseph Haydn: Missa in tempore belli ("Paukenmesse" Hob. XXII:9) / Michael Haydn: Requiem B-dur ("Opus Ultimum" Fragment) | Joseph Haydn, Michael Haydn; Helmuth Rilling, Gächinger Kantorei Stuttgart, Bach‐Collegium Stuttgart, Stuttgarter Kammerorchester | | 1 |
| 1998 | Chamber Music | Johann Michael Haydn; Piccolo Concerto Wien | | 1 |
| 1999 | The Art of the Baroque Trumpet, Volume 4 | Handel, Michael Haydn, Telemann; Niklas Eklund | | 1 |
| 1999 | 4 Symphonies | Michael Haydn; Franz Liszt Chamber Orchestra | | 1 |
| 2001 | Classical Trumpet Concertos | Hummel, Haydn, Leopold Mozart, Hertel, Michael Haydn; Crispian Steele‐Perkins, The King’s Consort, Robert King | | 1 |
| 2001 | Heiligste Nacht / Christmas Music | Joseph and Michael Haydn / Franz Xaver Gruber | | 1 |
| 2002 | Bassoon Concertos | Mozart, Michael Haydn, Stamitz, Weber; Laurence Perkins, Manchester Camerata, Douglas Boyd | | 1 |
| 2004 | Sacred Choral Works | Michael Haydn | | 1 |
| 2004 | Violin Concertos | W. A. Mozart, M. Haydn; Baiba Skride, Kammerorchester C.Ph.E.Bach, Hartmut Haenchen | | 1 |
| 2004 | Trombone Concertos | Leopold Mozart, Johann Michael Haydn, Gouinguené, Guilmant, Armin Rosin, Wiener Kammerorchester, Philippe Entremont | | 1 |
| 2005 | Requiem pro defuncto Archiepiscopo Sigismundo / Missa in honorem Sanctae Ursulae | Michael Haydn; Carolyn Sampson, Hilary Summers, James Gilchrist, Peter Harvey, Choir of the King’s Consort, The King’s Consort, Robert King | | 1 |
| 2005 | Andromeda e Perseo | Michael Haydn; Fodor, Asztalos, Szappanos, Gál, Savaria Symphony Orchestra, Tamás Pál | | 1 |
| 2006 | Geistliche Chormusik aus der Barockkirche Zwillbrock | Michael Haydn; Westfälische Kammersolisten, Markus Lehnert | | 1 |
| 2006 | Michael Haydn: Requiem in B / Mozart: Kleinere Kirchenwerke | Haydn, Mozart; KammerChor Saarbrücken, Kammerphilharmonie Mannheim, Georg Grün | | 1 |
| 2007 | Chamber Music for Double Bass | Rossini, Bottesini, Hoffmeister, Sperger, Michael Haydn; Gerhard Dzwiza | | 1 |
| 2007 | Joseph Haydn: Violin Concerto in C / Violin Concerto in G / Michael Haydn: Violin Concerto in A / Mozart: Adagio in E major / Rondo in C major | Joseph Haydn, Michael Haydn, Mozart; Arthur Grumiaux, Raymond Leppard, Edo de Waart | | 1 |
| 2009 | Orgelkonzert / 3 Sinfonien | Michael Haydn; Franz Lehrndorfer, Cappella Coloniensis, Wilfried Böttcher | | 1 |
| 2010 | Joseph & Michael Haydn | Joseph & Michael Haydn; Jasper de Waal, Concertgebouw Chamber Orchestra | | 1 |
| 2011 | Duo Sonatas | Wolfgang Amadeus Mozart, Michael Haydn; Rachel Podger, Jane Rogers | | 1 |
| 2012 | Flute Concertos & Scherzandi | F. J. & J. M. Haydn; Haydn‐Ensemble Berlin, Hansjörg Schellenberger, Emmanuel Pahud | | 2 |
| 2015 | Viola Concertos | Franz Anton Hoffmeister, Carl Stamitz, Michael Haydn; Andra Dārziņa, Jürgen Essl, Urban Camerata | | 1 |
| 2015 | Stolen Beauties | Mozart; Punto, Michael Haydn; Ironwood, Anneke Scott | | 1 |
| 2020 | Missa Sancti Nicolai Tolentini / Vesperae Pro Festo Sancti Innocentium / Anima Nostra | Michael Haydn; Harper, Owen, Charlston, Marko Sever, Lawes Baroque Players, St Albans Cathedral Girls Choir, Tom Winpenny | | 1 |
| 2021 | Motets | Anton Bruckner, Michael Haydn; MDR Leipzig Radio Choir, Philipp Ahmann | | 1 |
| — | Joseph Haydn: Missa Solemnis / Michael Haydn: Perfice gressus meos | Joseph Haydn, Michael Haydn; Collegium Cantorum St. Gallen, Südwestdeutsche Philharmonie Konstanz, Mario Schwarz | | 1 |
| — | J. Haydn: Horn Concerto no. 1 in D / Symphony no. 31 in D "Hornsignal" / M. Haydn: Horn Concerto in D | Joseph Haydn, Michael Haydn; Anthony Halstead, The Hanover Band, Roy Goodman | | 1 |
| — | Sacred Music + 2 Symphonies (Zürcher Sängerknaber, Zürcher Kammerorchester feat. conductor: Howard Griffiths) | Johann Michael Haydn; Zürcher Sängerknaben, Zürcher Kammerorchester, Howard Griffiths | | 1 |
| — | Trompetenkonzerte / Klarinettenkonzert | J. Haydn, M. Haydn, F.X. Richter, J. M. Molter | | 1 |
| — | Trompet Concertos | Joseph Haydn, Michael Haydn; Wolfgang Bauer, Württembergisches Kammerorchester Heilbronn, Ruben Gazarian | | 1 |
