Middleton moved to the New York City area in 1987, playing with the Bob Mintzer Big Band, the Lionel Hampton Big Band (who recorded a composition he wrote with his brother Rob Middleton entitled "Two Brothers" on "Cookin' in the Kitchen") and the Maria Schneider Jazz Orchestra. He founded his long-running quartet featuring at various times guitarist Ben Monder, drummers John Hollenbeck, Owen Howard, bassists Scott Colley and Peter Herbert, and pianists Henry Hey, Andy Ezrin, and David Berkman.
Middleton's first album, Acid Rain, featuring Joey Calderazzo, was released in 1991 by the French label Owl Records. His second, Terra Infirma was released in 1995 by EMI France, produced by David Liebman, and featuring the quartet of Middleton, pianist Renee Rosnes, bassist Paul Imm, and drummer Alan Jones augmented by a horn section.
The Fensters was a two saxophone, bass and drums formation featuring Middleton, Alan Jones, the saxophonist and composer François Theberge, and bassist Paul Imm. The Fensters recorded 2 CDs, "Jazz Music, Vol. 1" in 1992 for the Czech label Arta Records, and "Jazz Music, Vol. X" for the Dutch label Challenge Records sub-label A Records in 1996. In 1999 Middleton recorded his 3rd CD as a leader "Nomad's Notebook" with ECM Records guitarist Ralph Towner on acoustic guitars and piano, Dave Holland on bass, Alan Jones on drums, Noah Bless on trombone and Jamey Haddad on percussion. "Nomad's Notebook" was followed by his 2nd production for the German label Intuition Music and Media featuring trumpeter Kenny Wheeler and trombonist Nils Wogram entitled "Reinventing the World".