During the 90s he worked with the great drummer and member of the John Coltrane group of the mid-60's, Rashied Ali, touring globally and recording a well received album No One in Particular. Through this group, Gene met and played with Carlos Santana, Ravi Coltrane, Eddie Henderson, Archie Shepp, and Reggie Workman among many others.
Gene's last album, Modes of Limited Transcendence, has received great reviews globally. This album received the 2010 SESAC Outstanding Jazz Performance Award. This album features original compositions by Gene and pianist Tigran Hamasyan.
In 2012, Gene released a new album featuring vocals for the first time. The album titled A Thousand Summers was released on February 1, 2012. The music features Nicki Parrott on vocals and songs from the jazz canon arranged by Gene and Thomson Kneeland. The album features Gene Ess on guitar, Nicki Parrott on vocals, James Weidman on piano, Thomson Kneeland on bass, and Gene Jackson on drums.
Over his career, Gene has performed and recorded with many musicians. Some are Dave Liebman, Al Foster, Rashied Ali, Clark Terry, Slide Hampton, Carlos Santana, Archie Shepp, Reggie Workman, Tigran Hamasyan, and Ravi Coltrane. 
- One World Tribe, Prayer for September (Paddle Wheel King Records, 1995)
- Rashied Ali Quintet, No One in Particular (Survival Records, 2001)
- Gene Ess, Sunrise Falling (Amp Records, 2003)
- Gene Ess, Sandbox and Sanctum (SIMP Records, 2005)
- Gene Ess, Modes of Limited Transcendence (SIMP Records, 2008)
- Gene Ess, A Thousand Summers (SIMP Records, 2012)
- Gene Ess, Fractal Attraction(SIMP Records, 2013)