He worked with Art Blakey, Ornette Coleman, Pharoah Sanders, Dizzy Gillespie, Ellis Marsalis, Sonny Sharrock, Stanley Jordan, Wallace Roney, Arturo Sandoval, Courtney Pine, David Sanborn, David Sánchez, Dianne Reeves, Frank Lowe, Harry Connick, Jr., Herbie Hancock, Joe Henderson, Kenny Garrett, Kenny Kirkland, Kevin Eubanks, Lew Soloff, Manhattan Jazz Quintet, Melody Gardot, Mulgrew Miller and Tony Williams.

In 1987, Moffett signed with Blue Note and debuted as a leader that year with his first of three albums for the label, NetMan (1987) which featured Michael Brecker, Kenny Kirkland and Al Foster.

Three other '90s recordings for the Sweet Basil/Evidence label were done under the collective name of General Music Project (with saxophonist Kenny Garrett, pianists Geri Allen and Cyrus Chestnut, drummer Charles Moffett Sr, his father, known for his famous work with Ornette Coleman.

In 2001, Moffett released a tribute to the late Jaco Pastorius entitled Mr. P, a trio recording with pianist Mulgrew Miller and drummer Lewis Nash.

Joined by drummers Will Calhoun and Eric McPherson and Tibetan vocalist Yungchen Lhamo, the release references Asian and Middle Eastern influences.

To celebrate his thirtieth year as a recording artist, Moffett released his first live album, Music From Our Soul, also on Motéma, featuring his long time jazz compatriots Pharoah Sanders, Stanley Jordan, Cyrus Chestnut, Jeff "Tain" Watts, Victor Lewis and Mike Clarke.

In 2019, Moffett released Bright New Day in collaboration with the members of his touring band, violinist Scott Tixier, keyboardist Brian Jackson, drummer Mark Whitfield, Jr, and singer/guitarist Jana Herzen.