Eugene Stanley Ammons was born in Chicago on April 14, 1925, the son of boogie-woogie pianist Albert Ammons. He grew up inside the music rather than alongside it, and got his formal grounding at DuSable High School under Walter Dyett, the bandmaster whose classrooms also produced Nat King Cole, Johnny Griffin, and Von Freeman. Ammons was working professionally before he finished school: in 1943, at eighteen, he went on the road with trumpeter King Kolax's band.

In 1944 he joined Billy Eckstine's orchestra, the first big band built around the new bebop language, and stayed until 1947. Eckstine gave him the nickname that stuck when a shipment of straw hats ordered for the band would not fit Ammons's head, and "Jug" followed him for the rest of his life. The band put him next to Charlie Parker and Dizzy Gillespie, and later beside Dexter Gordon, with whom he cut the September 5, 1944 Deluxe single "Blowin' the Blues Away," a two-tenor exchange that became the model for the tenor-battle records Ammons would keep making for the next thirty years. He left in 1947 to lead his own group, which at Chicago's Jumptown Club included Miles Davis and Sonny Stitt, and scored a hit almost immediately with "Red Top," recorded in Chicago on June 19, 1947 and issued on Mercury 8048. In 1949 he replaced Stan Getz in Woody Herman's Second Herd. His 1950 reading of "My Foolish Heart" reached Billboard's Black pop chart, and from 1950 to 1952 he co-led a two-tenor band with Stitt whose March 5, 1950 Prestige recording of "Blues Up and Down" became one of the most copied performances of the era.

The mid-1950s put him at the center of Prestige's loose, blues-anchored jam-session records. The Happy Blues (Prestige PRLP 7039, recorded April 23, 1956) and Jammin' with Gene (July 13, 1956) gathered large casts around him: Donald Byrd and Art Farmer on trumpets, Jackie McLean on alto, Mal Waldron on piano, Doug Watkins and Art Taylor in the rhythm section. On January 3, 1958, at Rudy Van Gelder's Hackensack studio, he led a session that yielded two full albums, The Big Sound and Groove Blues, with John Coltrane on alto rather than his usual tenor, Paul Quinichette on tenor, Pepper Adams on baritone, and Jerome Richardson on flute. Later that year a narcotics conviction took him off the scene, and he served the first of two sentences, from 1958 to 1960.

He returned to Prestige in June 1960 and made the record he is still best known for. Boss Tenor, cut June 16, 1960 at Van Gelder's new Englewood Cliffs studio with Tommy Flanagan on piano, Doug Watkins on bass, Art Taylor on drums, and Ray Barretto on congas, is a quintet date built on tone and time, and its version of "Canadian Sunset" carried well beyond the jazz audience. The two years that followed were the densest of his career, driven in part by his need for cash and a heroin habit. He reunited with Sonny Stitt on Verve for Boss Tenors: Straight Ahead from Chicago (August 27, 1961) and Boss Tenors in Orbit! (February 18, 1962), recorded Up Tight! on October 18, 1961 with Patti Bown, George Duvivier, Art Taylor, and Barretto, and then in a five-month run from April to September 1962 taped the sessions behind Soul Summit Vol. 2, The Soulful Moods of Gene Ammons, Blue Groove, Preachin', Jug & Dodo, Velvet Soul, Sock!, and, on September 9, Bad! Bossa Nova, with Hank Jones, Kenny Burrell, and Bucky Pizzarelli. A second narcotics conviction late that year sent him to Joliet penitentiary for seven years. Prestige spent the rest of the decade releasing the backlog, which is why albums such as Velvet Soul (1964) and Angel Eyes (1965) reached the shops years after the tape was rolled.

Ammons was released in 1969 and signed what Prestige owner Bob Weinstock described as the largest contract the label had ever offered. The Boss Is Back!, recorded November 10 and 11, 1969 with Junior Mance, Buster Williams, Bernard Purdie, and Candido, reached No. 174 on the Billboard Top LPs chart, and the same two days also produced Brother Jug!. His 1970s work leaned harder into organ combos, electric bass, and funk rhythm sections: "Jungle Strut" (1970), The Black Cat! and My Way (1971), Free Again (1972), Big Bad Jug (1973). The tenor battles continued alongside it, on the live The Chase! with Dexter Gordon, taped July 26, 1970 at Chicago's North Park Hotel with two local rhythm sections including bassist Cleveland Eaton, and on You Talk That Talk! with Stitt in February 1971. He played the Montreux Jazz Festival in 1973, documented on Gene Ammons and Friends at Montreux.

His last studio session ran March 18 to 20, 1974 in New York, with Nat Adderley, Gary Bartz, Kenny Drew, Sam Jones, Louis Hayes, and Ray Barretto. He was already ill with bone cancer, and the album was issued posthumously as Goodbye. Gene Ammons passed away in Chicago on August 6, 1974, at 49, of bone cancer and pneumonia, and was buried at Lincoln Cemetery in Blue Island, Illinois.

Ammons built his playing on sound first. Where most of his bebop contemporaries pursued intricate line-running, he favored big gestures, wide vibrato, and scooped blues phrasing that put the weight on each note rather than on the number of them, an approach traceable to Lester Young's phrasing and Ben Webster's tone and pushed toward rhythm and blues. That combination made him a founder of the Chicago tenor school alongside Von Freeman, and one of the direct sources of soul jazz, the idiom that later carried Stanley Turrentine, Houston Person, and a generation of organ-combo tenors. He was equally at home in two settings that rarely overlap: the competitive two-tenor format, where his sound had to stand up to Dexter Gordon, Sonny Stitt, or the crowded January 1958 Prestige date that had John Coltrane playing alto and Pepper Adams on baritone beside him, and the slow ballad, where he could hold a melody almost straight and still make it his. Critics have consistently placed the ballads and Boss Tenor at the top of his catalog; Scott Yanow, reviewing the 1969 comeback album, wrote that his "huge sound was unchanged" after seven years away from a bandstand.