Geri Antoinette Allen was born June 12, 1957, in Pontiac, Michigan, and raised in Detroit, where her father worked as a school principal. She took up piano at age seven and received her formative jazz education at Cass Technical High School under the mentorship of trumpeter Marcus Belgrave, a central figure in the city's postwar jazz scene. In 1979 she earned a bachelor's degree in jazz studies from Howard University in Washington, D.C., one of the program's early graduates.

After Howard, Allen moved to New York and studied privately with pianist Kenny Barron, who later recalled her as a student who "heard some things musically that others did not." On the advice of educator Nathan Davis, she then enrolled at the University of Pittsburgh, earning a master's degree in ethnomusicology in 1982 before returning to New York. There she fell in with the Brooklyn-based M-Base collective surrounding saxophonist Steve Coleman, appearing on his 1985 album Motherland Pulse. Her own recording debut as a leader, The Printmakers (1984, Minor Music), was a trio session with bassist Anthony Cox and drummer Andrew Cyrille billed to the Geri Allen Trio; a second Minor Music leader date, Home Grown, followed in 1985.

Through the late 1980s and into the 1990s Allen built a rich body of work as both leader and collaborator. She formed a trio with bassist Charlie Haden and drummer Paul Motian, documented on Etudes (1988, Soul Note), and signed with Blue Note Records, releasing Triangular (1989), The Nurturer (1990, reuniting her with Belgrave alongside Kenny Garrett, Robert Hurst and Jeff "Tain" Watts), and Maroons (1992). Her 1994 trio album Twenty One, recorded with bassist Ron Carter and drummer Tony Williams, brought her the inaugural Soul Train Lady of Soul Award for a jazz album. In 1996 she became the first woman and the youngest musician to receive Denmark's Jazzpar Prize, one of the field's most prestigious international honors, and that same year she recorded with Ornette Coleman on his Sound Museum sessions and portrayed pianist Mary Lou Williams in Robert Altman's film Kansas City. She moved to Verve for The Montreal Tapes (1997) and The Gathering (1998).

The 2000s brought a run of trio and quartet dates for Japanese and American labels, including a live recording with Motian and Haden for DIW, and, after signing with Telarc, The Life of a Song (2004, with Dave Holland and Jack DeJohnette) and Timeless Portraits and Dreams (2006, a collection of spirituals and bebop tunes with Ron Carter, Jimmy Cobb, and a guest appearance by trumpeter Wallace Roney, to whom she was married from 1995 to 2008). She composed the suite "For the Healing of the Nations" (2006), honoring the victims of September 11, performed with Howard University's Afro Blue choir, and in 2008 received a Guggenheim Fellowship to compose an original solo piano work honoring Cecil Taylor, McCoy Tyner, and Herbie Hancock. Alongside her performing career she taught for a decade at the University of Michigan and held faculty posts at Howard University and the New England Conservatory.

Allen's later recordings appeared mainly on the Motéma label: the Guggenheim-funded Flying Toward the Sound (2010), named a best-of-year pick by NPR and DownBeat's critics; the holiday album A Child Is Born (2011); Secret of the Wind (2012), a duo record with vocalist Elisabeth Kontomanou; and Grand River Crossings: Motown & Motor City Inspirations (2013), a tribute to her native Detroit. In 2013 she succeeded Nathan Davis as Director of Jazz Studies at the University of Pittsburgh, her alma mater, a post she held until her death. She received an honorary Doctorate of Music from Berklee College of Music in 2014 and the Congressional Black Caucus Foundation's Jazz Legacy Award the same year. She continued to break new collaborative ground with the trio ACS (with Terri Lyne Carrington and Esperanza Spalding) and the bass-less MAC Power Trio with David Murray and Carrington, whose album Perfection (recorded 2015, released 2016) closed with an arrangement of an unrecorded Ornette Coleman composition. That same year she received a Grammy nomination for her work producing the expanded reissue of Erroll Garner's The Complete Concert by the Sea.

Geri Allen died of complications from cancer on June 27, 2017, in Philadelphia, two weeks after her 60th birthday. She was survived by her father, her brother, and her three children. In 2022 she was voted into the DownBeat Hall of Fame, and in 2023 Motéma released A Lovesome Thing, a posthumous duo recording with guitarist Kurt Rosenwinkel captured live in Paris in 2012.

Allen was one of the most versatile pianists of her generation, equally at home in the acoustic hard-bop tradition and in the freer, funk- and world-music-inflected language of the M-Base movement she helped define alongside Steve Coleman. Her playing combined a loose-limbed, harmonically adventurous lyricism with a percussive, rhythmically independent left hand, qualities that let her move convincingly between the drummerless intimacy of a piano trio, the collective improvisation of Ornette Coleman's harmolodic music, and the gospel- and blues-rooted material of her Detroit- and spirituals-themed later projects. She was also an important bandleader for other women in jazz, forming high-profile trios with Terri Lyne Carrington and Esperanza Spalding (ACS) and mentoring younger musicians through her teaching posts and through NJPAC's all-female jazz residency program.