| 1970 | Nation Time | Joe McPhee | | 4 |
| 1972 | Trinity | Joe McPhee | | 2 |
| 1974 | Pieces of Light | Joe McPhee & John Snyder | | 2 |
| 1975 | Black Magic Man | Joe McPhee | | 1 |
| 1977 | Rotation | Joe McPhee | | 1 |
| 1977 | Tenor | Joe McPhee | | 1 |
| 1980 | Old Eyes | Joe McPhee | | 1 |
| 1981 | Topology | Joe McPhee | | 2 |
| 1981 | Tales and Prophecies | André Jaume, Joe McPhee & Raymond Boni | | 1 |
| 1985 | Visitation | Joe McPhee with The Bill Smith Ensemble | | 2 |
| 1992 | Impressions of Jimmy Giuffre | Joe McPhee | | 1 |
| 1993 | River Station | Jimmy Giuffre - André Jaume With Guest Joe McPhee | | 1 |
| 1995 | Sweet Freedom - Now What? | Joe McPhee / Lisle Ellis / Paul Plimley | | 1 |
| 1998 | A Meeting in Chicago | Joe McPhee, Ken Vandermark & Kent Kessler | | 1 |
| 1998 | As Serious as Your Life | Joe McPhee | | 1 |
| 1998 | CIMPhonia 1998, Part 1 | Joe McPhee, Mark Whitecage, Paul Smoker, David Prentice, Peter Kowald, Dominic Duval, Jay Rosen | | 1 |
| 1999 | CIMPhonia 1998, Part 2 | Joe McPhee - Mark Whitecage - Paul Smoker - David Prentice - Peter Kowald - Dominic Duval - Jay Rosen | | 1 |
| 1999 | The Dream Book | Joe McPhee / Dominic Duval | | 1 |
| 1999 | Zebulon | Michael Bisio & Joe McPhee | | 1 |
| 2000 | Undersound | Dominic Duval / John Heward / Joe McPhee | | 1 |
| 2000 | Emancipation Proclamation: A Real Statement Of Freedom | Hamid Drake / Joe McPhee | | 1 |
| 2000 | Grand Marquis | Joe McPhee, Johnny McLellan | | 1 |
| 2000 | No Greater Love | Joe McPhee / Joe Giardullo / Michael Bisio / Dominic Duval | | 1 |
| 2001 | Specific Gravity | Joe McPhee & Joe Giardullo | | 1 |
| 2001 | She Knows… | The Thing w/ Joe McPhee | | 2 |
| 2002 | Sustain | Mat Maneri featuring Joe McPhee | | 1 |
| 2002 | Chicago Tenor Duets | Evan Parker / Joe McPhee | | 1 |
| 2003 | Undersound II | Dominic Duval / John Heward / Joe McPhee | | 1 |
| 2004 | Tales Out of Time | Peter Brötzmann, Joe McPhee, Kent Kessler & Michael Zerang | | 1 |
| 2005 | Remembrance | Joe McPhee, Michael Bisio, Raymond Boni, Paul Harding | | 1 |
| 2006 | Guts | Peter Brötzmann, Joe McPhee, Kent Kessler & Michael Zerang | | 1 |
| 2008 | Intimate Conversations | Joe McPhee, Mikołaj Trzaska, Jay Rosen | | 1 |
| 2009 | Magic | McPhee / Duval / Rosen / Trzaska | | 1 |
| 2009 | The Damage Is Done | Joe McPhee, Peter Brötzmann, Kent Kessler & Michael Zerang | | 1 |
| 2010 | Blue Chicago Blues | Joe McPhee & Ingebrigt Håker Flaten | | 1 |
| 2010 | Sound on Sound (Solo 1968-1973) | Joe McPhee | | 1 |
| 2011 | Creole Gardens (A New Orleans Suite) | Joe McPhee / Michael Zerang | | 1 |
| 2011 | Ibsen’s Ghosts | Joe McPhee, Jeb Bishop, Ingebrigt Håker Flaten, Michael Zerang | | 1 |
| 2011 | OTO | Decoy & Joe McPhee | | 1 |
| 2012 | Brooklyn DNA | Joe McPhee & Ingebrigt Håker Flaten | | 2 |
| 2012 | Ithaca | Joe McPhee / Eli Keszler | | 1 |
| 2012 | Scraps and Shadows | Joe McPhee & Chris Corsano | | 1 |
| 2013 | Human Encore | Trespass Trio + Joe McPhee | | 1 |
| 2013 | Sonic Elements (For Pocket Trumpet and Alto Saxophone) | Joe McPhee | | 1 |
| 2014 | Spontaneous Combustion | Decoy with Joe McPhee | | 1 |
| 2014 | Nine Ways to Read a Bridge | Ken Vandermark Duos W/ Agustí Fernández - Christof Kurzmann - Joe McPhee - Joe Morris Trios W/ Paul Lytton - Nate Wooley - Eddie Prévost - John Tilbury | | 1 |
| 2015 | If You Have Time | Konstrukt & Joe McPhee | | 3 |
| 2015 | To Be Continued | Joe McPhee & John Snyder | | 1 |
| 2015 | This Is Our Language | Rodrigo Amado, Joe McPhee, Kent Kessler & Chris Corsano | | 1 |
| 2015 | Ticonderoga | Joe McPhee, Jamie Saft, Joe Morris & Charles Downs | | 2 |
| 2015 | Chance Meeting | Joe McPhee, Graham Lambkin | | 1 |
| 2015 | Soul Stream | Michiyo Yagi / Joe McPhee / Paal Nilssen-Love / Lasse Marhaug | | 2 |
| 2015 | Alone Together: The Solo Ensemble Recordings 1974 & 1979 | Joe McPhee | | 1 |
| 2015 | Solos : The Lost Tapes (1980 - 1981 - 1984) | Joe McPhee | | 1 |
| 2016 | Bricktop | Joe McPhee & Ingebrigt Håker Flaten | | 1 |
| 2016 | 15.2.16 | Chris Corsano, Eddie Prévost, Joe McPhee, Orphy Robinson | | 1 |
| 2016 | Nuclear Family | Joe McPhee & André Jaume | | 1 |
| 2017 | Seattle Symphony | Joe McPhee | | 1 |
| 2017 | My Undocumented Alien Clarinet | Joe McPhee & Bryan Eubanks | | 1 |
| 2018 | A History of Nothing | Rodrigo Amado, Joe McPhee, Kent Kessler & Chris Corsano | | 1 |
| 2018 | Keep Going | Joe McPhee & Hamid Drake | | 1 |
| 2019 | Largest Afternoon | Ken Vandermark, Arto Lindsay, Joe McPhee, Phil Sudderberg | | 1 |
| 2019 | Invitation to a Dream | Susan Alcorn, Joe McPhee, Ken Vandermark | | 2 |
| 2020 | AC / DC | Decoy with Joe McPhee | | 2 |
| 2020 | Black Is the Color | Joe McPhee | | 1 |
| 2020 | Harmonia Macrocosmica | Joe McPhee / Lasse Marhaug | | 1 |
| 2021 | Sala Rossa - 2001 | Joe McPhee, Joe Giardullo, John Heward & Nicolas Caloia | | 1 |
| 2021 | ERA | Joe McPhee & Joe Morris | | 1 |
| 2021 | Blue Reality Quartet! | Michael Marcus, Joe McPhee, Jay Rosen & Warren Smith | | 1 |
| 2023 | Sometimes the Air Is | Steve Swell, Joe McPhee & Chris Corsano | | 1 |
| — | Novio Iolu: Music for a New Place | Jérôme Bourdellon / Joe McPhee | | 1 |
| — | Reqiphoenix Nexus | The C.T. String Quartet With Joe McPhee | | 1 |
