Dafnis Prieto was born July 31, 1974, in Santa Clara, Cuba, a town about 150 miles from Havana. He studied guitar and percussion as a boy, then moved to Havana in his teens to attend the National School of Music (Escuela Nacional de Arte), where he trained in classical and Afro-Cuban percussion before jazz took hold of him; he graduated in 1992 from a cohort that also included saxophonist Yosvany Terry. In 1997 the two co-founded the Havana group Columna B with pianist Roberto Carcassés, and while still based in Cuba, Prieto was invited north by the Canadian saxophonist Jane Bunnett to perform with her group, his first exposure to playing in North America.

Prieto moved permanently to New York City in 1999 at age twenty-five. He quickly became one of the city's most sought-after drummers, working as a sideman for Eddie Palmieri, Michel Camilo, Carlos Barbosa-Lima, Dave Samuels, and Arturo O'Farrill, and appearing on Caribbean Jazz Project's The Gathering (2002) and Birds of a Feather (2003), where he also contributed original compositions. He simultaneously moved in more exploratory circles, becoming the founding drummer of Henry Threadgill's ensemble Zooid, heard on Up Popped the Two Lips (2001) and Everybodys Mouth's a Book (2001). In the early 2000s he formed his own quintet with trumpeter Brian Lynch, saxophonist Peter Apfelbaum, bassist Hans Glawischnig, and pianist Luis Perdomo, a band built to carry his own compositions rather than side work.

That quintet's music became About the Monks, released in February 2005 on the independent Zoho label, Prieto's debut as a leader; he wrote, arranged, and produced the record himself. Absolute Quintet followed on Zoho in 2006, expanding the working band's palette with cello and violin and featuring a guest appearance from Threadgill on alto saxophone. Recognition followed quickly: Absolute Quintet drew a 2007 Grammy nomination for Best Latin Jazz Album, and the same year brought a Latin Grammy nomination for Best New Artist. From 2005 to 2014 Prieto served on the jazz faculty at New York University, and in 2011 he was named a MacArthur Fellow, the foundation's citation crediting him with infusing Latin jazz "with a bold new energy and sound."

Around 2008 Prieto launched his own label, Dafnison Music, beginning with Taking the Soul for a Walk, credited to the Dafnis Prieto Sextet with saxophonists Yosvany Terry and Peter Apfelbaum, pianist Manuel Valera, bassist Yunior Terry, and, in the trumpet chair, Avishai Cohen. He formed a second working band, the Sí o Sí Quartet, documented on Live at Jazz Standard NYC (2009) with Manuel Valera, Apfelbaum, and bassist Charles Flores, and led a trio session, Proverb Trio (2012), with keyboardist Jason Lindner and vocalist Kokayi. The Sextet returned on Triangles and Circles (2015).

Prieto assembled a big band for Back to the Sunset, released on Dafnison Music in 2018 with a roster that included saxophonists Peter Apfelbaum, Roman Filiu, Chris Cheek and Joel Frahm and pianist Manuel Valera; the album won the Grammy Award for Best Latin Jazz Album in February 2019 and also drew a Latin Grammy nomination that year. He moved to the Frost School of Music at the University of Miami in 2015, where he continues to teach and direct the Frost Latin Jazz Orchestra, and published the first of three books on rhythm, A World of Rhythmic Possibilities, in 2016. The Sextet's Transparency (2020) brought a further Grammy nomination for Best Latin Jazz Album in 2021.

Cantar (2022), a duo record with the Brazilian vocalist Luciana Souza, moved Prieto into unaccompanied song settings, and 3 Sides of the Coin (2024), a reunion of the Sí o Sí Quartet with pianist Martin Bejerano and bassist Ricardo Rodríguez, marked twenty-five years since his move to the United States and earned a DownBeat Editors' Pick review. In 2026 he recorded Fifteen for Nonesuch Records, a co-led trio session with pianist Vijay Iyer and Henry Threadgill, returning the favor of Threadgill's own guest turns on Absolute Quintet and Back to the Sunset by putting the two of them in a band together as equals.

Prieto's signature is the transposition of Afro-Cuban folkloric vocabulary, the layered patterns of rumba and son, conga and timbale phrasing, directly onto a standard jazz drum kit, played with a level of polyrhythmic density and speed that few other drummers have attempted on the instrument. His stated influences run from American drummers Art Blakey and Elvin Jones to the Latin percussion tradition of Ray Barretto, Mongo Santamaria, and Tito Puente, and Blakey's example shaped him as a bandleader and arranger as much as a player: Prieto's own small-group writing echoes the message-driven, horn-forward arranging of Blakey's Jazz Messengers, filtered further through the example of Eddie Palmieri's bandleading in Afro-Cuban jazz. Critics have consistently singled out his compositions as inseparable from his drumming, each instrumental role, groove, and metric shift built to serve a larger rhythmic idea rather than to showcase technique for its own sake. Alongside his performing career, Prieto has become an influential teacher of Afro-Cuban rhythm, publishing three instructional books between 2016 and 2025 and directing the Frost Latin Jazz Orchestra at the University of Miami since 2015.