As leader
- Golden Saxophone (Savoy, 1952)
- All Star Sessions (Prestige, 1950-55) – with Sonny Stitt
- The Happy Blues (Prestige, 1956)
- Jammin’ with Gene (Prestige, 1956)
- Funky (Prestige, 1957)
- Jammin’ in Hi Fi with Gene Ammons (Prestige, 1957) – also released as The Twister
- The Big Sound (Prestige, 1958)
- Groove Blues (Prestige, 1958)
- Blue Gene (Prestige, 1958)
- The Swingin’est (Vee-Jay, 1958) – with Bennie Green
- Boss Tenor (Prestige, 1960)
- Nice an’ Cool (Moodsville, 1961)
- Jug (Prestige, 1961)
- Groovin’ with Jug (Pacific Jazz, 1961) – with Richard “Groove” Holmes
- Dig Him! (Argo, 1961) – with Sonny Stitt – also released as We’ll Be Together Again (Prestige)
- Boss Tenors (Verve, 1961) – with Sonny Stitt
- Just Jug (Argo, 1961) – also released as Gene Ammons Live! in Chicago (Prestige)
- Up Tight! (Prestige, 1961)
- Boss Soul! (Prestige, 1961)
- Twisting the Jug (Prestige, 1961) – with Joe Newman and Jack McDuff
- Brother Jack Meets the Boss (Prestige, 1962) – with Jack McDuff
- Boss Tenors in Orbit! (Verve, 1962) – with Sonny Stitt
- Soul Summit (Prestige, 1962) – with Sonny Stitt and Jack McDuff
- Late Hour Special (Prestige, 1961-62 [1964])
- The Soulful Moods of Gene Ammons (Moodsville, 1962)
- Blue Groove (Prestige, 1962 [1982])
- Preachin’ (Prestige, 1962)
- Jug & Dodo (Prestige, 1962 [1972]) – with Dodo Marmarosa
- Velvet Soul (Prestige, 1960-62 [1964])
- Angel Eyes (Prestige, 1960-62 [1965])
- Sock! (Prestige, 1954-62 [1965])
- Bad! Bossa Nova (Prestige, 1962)
- The Boss Is Back! (Prestige, 1969)
- Brother Jug! (Prestige, 1969)
- Night Lights (Prestige, 1970)
- The Chase! (Prestige, 1970) – with Dexter Gordon
- The Black Cat! (Prestige, 1970)
- You Talk That Talk! (Prestige, 1971) – with Sonny Stitt
- My Way (Prestige, 1971)
- Chicago Concert (Prestige, 1971) – with James Moody
- Free Again (Prestige, 1972)
- Got My Own (Prestige, 1972)
- Big Bad Jug (Prestige, 1972)
- God Bless Jug and Sonny (Prestige, 1973 [2001]) – with Sonny Stitt
- Left Bank Encores (Prestige, 1973 [2001]) – with Sonny Stitt
- Gene Ammons and Friends at Montreux (Prestige, 1973)
- Gene Ammons in Sweden (Enja, 1973)
- Brasswind (Prestige, 1973)
- Together Again for the Last Time (Prestige, 1973) – with Sonny Stitt
- Goodbye (Prestige, 1974)
As sideman
With Charles Mingus
- Charles Mingus and Friends in Concert (Columbia, 1972)
With Sonny Stitt
- Kaleidoscope (Prestige, 1950 [1957])
- Stitt’s Bits (Prestige, 1950 [1958])