| 1987 | Mass in D minor, HOB XXII:11 "Lord Nelson Mass" | Haydn; Banchetto Musicale, Martin Pearlman | | 1 |
| 1992 | Solemn Vespers of the Confessor, K. 339 / Mass in C, K. 317 | Mozart; Banchetto Musicale, Martin Pearlman | | 1 |
| 1992 | Concerti Grossi, op. 6, nos. 1-6 | Handel; Boston Baroque, Martin Pearlman | | 1 |
| 1992 | Messiah | Georg Friedrich Händel; Boston Baroque, Martin Pearlman, Karen Clift, Catherine Robbin, Bruce Fowler, Victor Ledbetter | | 2 |
| 1993 | Brandenburg Concertos nos. 4, 5 & 6 | Bach; Boston Baroque, Martin Pearlman | | 1 |
| 1994 | Brandenburg Concertos nos. 1, 2, & 3 | Johann Sebastian Bach; Boston Baroque, Martin Pearlman | | 1 |
| 1995 | Requiem | Mozart; Martin Pearlman, Boston Baroque, Ruth Ziesak, Nancy Maultsby, Richard Croft, David Arnold | | 1 |
| 1996 | Dido and Aeneas and Music for Plays & Masques | Purcell; Nancy Maultsby, Susannah Waters, Russell Braun, Laura Tucker, Richard Clement, Sharon Baker, Boston Baroque, Martin Pearlman | | 1 |
| 1997 | Vespers of 1610 | Claudio Monteverdi; Boston Baroque, Martin Pearlman | | 1 |
| 1998 | Lost Music of Early America: Music of the Moravians | Boston Baroque, Martin Pearlman | | 1 |
| 2000 | Iphigénie en Tauride | Christoph Willibald Gluck; Boston Baroque, Martin Pearlman | | 1 |
| 2000 | Mass in B minor | Bach; Martin Pearlman, Boston Baroque | | 1 |
| 2002 | Mozart’s Circle: The Beneficent Dervish - Mozart: The Impresario, K. 486 | Mozart, Henneberg; Benedikt Schack, Franz Xaver Gerl, Boston Baroque, Martin Pearlman, Cyndia Sieden, Sharon Baker, John Aler, Kevin Deas, Alan Ewing & Deanne Meek | | 1 |
| 2003 | Music for the Royal Fireworks / Water Music | Handel; Boston Baroque, Martin Pearlman | | 1 |
| 2004 | The Complete Orchestral Suites | J. S. Bach; Boston Baroque, Martin Pearlman | | 1 |
| 2005 | Flute Concertos / Symphony no. 41 “Jupiter” | Mozart; Jacques Zoon, Boston Baroque, Martin Pearlman | | 1 |
| 2006 | Vivaldi: Gloria / Bach: Magnificat | Antonio Vivaldi, Johann Sebastian Bach; Martin Pearlman. Boston Baroque | | 1 |
| 2007 | Requiem | Luigi Cherubini; Boston Baroque, Martin Pearlman | | 1 |
| 2008 | Concerti grossi, Op. 6 Nos. 7-12 | Handel; Boston Baroque & Martin Pearlman | | 1 |
| 2009 | The Four Seasons | Vivaldi, Geminiani; Boston Baroque, Martin Pearlman, Christina Day Martinson | | 2 |
| 2012 | The Creation (Die Schöpfung) | Joseph Haydn; Boston Baroque, Martin Pearlman, Amanda Forsythe, Keith Jameson, Kevin Deas | | 2 |
| 2015 | Il ritorno d'Ulisse in patria | Claudio Monteverdi; Martin Pearlman & Boston Baroque | | 1 |
