Gene Ess was born Gene Shimosato in Tokyo and raised on an American air base in Okinawa, which gave him three separate musical educations at once: piano lessons in the European classical repertoire, the indigenous Okinawan music around him, and the jazz and pop coming out of the service clubs where American personnel drank. By 14 he was working, playing clubs and festivals across Okinawa. He came to the United States for university, studying classical guitar at George Mason University with Larry Snitzler, a pupil of Andres Segovia, and orchestral composition with Glenn Smith. In 1983 a performance of Lennox Berkeley's "Theme and Variations" won him an Outstanding Performance Award from DownBeat and a scholarship to the Berklee College of Music. (A 2018 press biography puts the DownBeat award in 1984; Ess's own site says 1983.)

Berklee is where the classical guitarist became a jazz musician. He studied with saxophonist Jerry Bergonzi and with Charlie Banacos, the private teacher whose ear-training and improvisation curriculum passed through most of that generation of Boston players, and he fixed on John Coltrane as the reference point he has cited ever since. He graduated with honors in 1990 and moved to New York in 1991, arriving late to jazz by the standards of the scene he was joining and roughly a decade older than the usual first-year New York arrival.

What happened next is the reason his name turns up in Coltrane-adjacent discographies. Ess joined the band of drummer Rashied Ali, Coltrane's last drummer, and toured with him through the early 1990s. On June 25, 1992, at The Studio on Greene Street in lower Manhattan, Ali convened a quintet that has become one of the better-known unreleased-then-released sessions of the period: Ess on guitar, Ravi Coltrane on tenor and soprano, Matthew Garrison on bass, Greg Murphy on piano, Ali on drums. The tapes sat for nine years and came out in 2001 as No One in Particular on Ali's own Survival Records. Ess is billed on that sleeve as Gene Shimosato, is credited as co-producer alongside Ali, and shot the band photograph; it is the only commercially issued recording that carries his birth name rather than his professional one. A European run by the same group is reported to have shared bills with Carlos Santana and Archie Shepp, and both men appear in every capsule biography Ess has published since.

His own recording career began in Japan rather than New York. In 1995 King Records issued Prayer for September on its Paddle Wheel jazz imprint, billed to One World Tribe, a Japanese-American band King's own catalogue copy describes as led by "Gene Shimosato, from Okinawa, active in New York." Ravi Coltrane returned on soprano and tenor, with Takuya Nakamura on piano and trumpet, Lonnie Plaxico on bass, and Tony Moreno on drums. The record is essentially invisible in the English-language jazz databases and does not appear on Discogs or in the Wikipedia article about him, but it is the first album he led, it stayed in print in Japan, and King reissued it digitally in 2025. Eight years later, Sunrise Falling (2003) picked up the New York thread instead, an electric record of guitars, synthesizers and loops with Matthew Garrison and Fima Ephron splitting the bass chair and Jo Jo Mayer and Rashied Ali splitting the drums.

From 2005 Ess ran his own label, SIMP Records, out of an address in Ridgewood, Queens, and the run of albums that followed is his real body of work. Sandbox and Sanctum: Song Cycle for Quartet (2005) put him with Donny McCaslin on tenor and soprano, Harvie S on bass and Gene Jackson on drums, and carried a dedication to his son, Ryo Shimosato, whose name recurs across three later album titles. Modes of Limited Transcendence (2008) hired the 21-year-old Tigran Hamasyan on piano and Rhodes and Tyshawn Sorey on drums, several years before either was widely known outside New York, and took the 2010 SESAC Outstanding Jazz Performance Award. A Thousand Summers (2012) broke the pattern entirely: ten standards arranged by Ess and bassist Thomson Kneeland for the Australian singer and bassist Nicki Parrott, with James Weidman on piano and Gene Jackson on drums.

In 2013 he launched Fractal Attraction, a quintet of voice, guitar, piano, bass and drums built around vocalist Thana Alexa singing melody lines in syllables rather than lyrics, using the voice as a front-line horn. Four albums came out of it over five years: Fractal Attraction (2013), which reached number three on the American jazz radio charts, Eternal Monomyth (2015), Absurdist Theater (2016), whose eight pieces are built on Camus and the absurdist premise that a person should accept an absurd condition and go looking for meaning anyway, and Apotheosis (2018), which takes its title from Joseph Campbell. The rhythm sections turned over across the four (David Berkman, John Escreet, Manuel Valera and Sebastien Ammann on piano; Kneeland, then Yasushi Nakamura on bass; Gene Jackson, then Clarence Penn on drums) while Alexa and Ess stayed constant. After a four-year gap Ess returned with Ah-Bop (2022), written while he was stranded in Tokyo during the pandemic and cut in New York with Scott Colley and Clarence Penn: his first record in the bare guitar-bass-drums trio format, and the one he framed against the trios of John McLaughlin, Jim Hall and Pat Martino. He continues to work as a leader, producer and teacher, dividing his time between New York and Japan, where he plays regularly in Tokyo and Yokohama.

Ess plays with an unusually clean, unsaturated tone for a guitarist working in an electric post-bop context, and his writing shows the two educations that preceded jazz for him: the through-composed classical forms he studied at George Mason and the modal, ritual repetition of Okinawan and Japanese traditional music, which shows up in titles like "Gagaku Dreams," "Kerama Processional" and "Sun Matsuri." He calls his albums song cycles and means it in the Schubertian sense, linking movements by motive and key rather than assembling a set of unrelated tunes. John Coltrane has been his stated reference point since Berklee, and the debt is structural rather than imitative: Olivier Messiaen's modes of limited transposition (which gave one album its punning title) and Coltrane's late modal practice pull in the same direction for him. His most distinctive idea as a bandleader is the use of the wordless voice as a horn, the organizing principle of the Fractal Attraction quintet, which the jazz press treated as the interesting thing about the band; JazzTimes called the group "a unit of remarkable means and resilience." As a guitarist he cites John McLaughlin, Jim Hall and Pat Martino, and, less predictably, the Japanese metal band Babymetal.