He was born in Rocky Mount, North Carolina and studied at Virginia State College, but indicated that he learned more from musicians he worked with. In the seventies he played with Roy Haynes, Freddie Hubbard, Woody Shaw and Billy Harper, among others.
- Triangle (Whynot Records, 1975)
- The Lifesaver (Muse Records, 1975)
- Angel Eyes (Muse Records, 1976)
- Parade (SteepleChase Records, 1979)
- Impressions of Copenhagen (Theresa Records, 1981)
- Devotion (SteepleChase, 1983)
- Suburban Fantasies (SteepleChase, 1983) with Johnny Dyani
- Suite for Chocolate (SteepleChase, 1985) with Jesper Lundgaard
- New Life (SteepleChase, 1986)
- New Beginnings (Evidence, 1988)
- Wherebutterflies Play (Perea Productions, 1992)
- P.S. I Love You (Perea Productions, 2000)
- Monkisms (Capri, 2000)
- Lights Out (The Bonner Party, Akashic Records, 2001)
- Happy Talk (Perea Productions, 2002)
- Current Events (Cherry Sound Records, 2013)
With Richard Davis
- Epistrophy & Now's the Time (Muse, 1972)
With Billy Harper
- Black Saint (Black Saint, 1975)
With Azar Lawrence
- Bridge into the New Age (Prestige, 1974)
With Pharoah Sanders
- Black Unity (Impulse!, 1971)
- Live at the East (Impulse!, 1972)
- Village of the Pharoahs (Impulse!, 1973)
- Elevation (Impulse!, 1973)
- Love in Us All (Impulse!, 1972–73)
- Journey to the One (Theresa, 1980)
- Rejoice (Theresa, 1981)
With Woody Shaw
- Love Dance (Muse, 1975)
With Harold Vick
- Don't Look Back (Strata-East, 1974)
With The Visitors
- Motherland (Muse Records, 1975)
With Stephanie Hancock
- This Happy Madness (DaJazz Records, 2001)
- Jeff Tamarkin (1 December 2014). "Pianist Joe Bonner Dies at 66". Jazz Times. Retrieved 31 May 2015.
- "Joseph Bonner, Jr. Obituary". Retrieved 31 May 2015.
- "Joe Bonner @ All About Jazz". All About Jazz. Retrieved 31 May 2015.
- "Joe Bonner". All About Jazz. Retrieved 2009-12-31.
- Yanow, Scott. "Joe Bonner Biography". Allmusic. Retrieved 3 April 2010.