Manuel Valera was born in Havana on October 17, 1980, into the music. His father, the saxophonist and flautist Manuel Valera Sr., played in Gonzalo Rubalcaba's Grupo Proyecto and on the Havana recordings that came out of it, including the concert Dizzy Gillespie gave at the fifth Jazz Plaza festival in 1985, and later recorded with Chucho Valdés, Cachao and Paquito D'Rivera. The son began at Havana's Manuel Saumell Conservatory as a classical saxophone major. He did not become a pianist until the family emigrated to the United States in December 1994, when he was fourteen; he finished school at South Broward High School in Hollywood, Florida, and switched instruments in the process.

He moved to New York around 2000 to enter the jazz program at the New School, where his teachers included Reggie Workman, George Garzone, Jane Ira Bloom, Gerard D'Angelo and Richie Beirach. He began writing that same year, and the writing has driven the career since. His first record as a leader, Forma Nueva, was cut in late October 2003, two days after his twenty-third birthday, and issued in 2004 on Mavo Records, the label he still runs. It is an unusually well-appointed debut: John Patitucci on bass throughout, with Bill Stewart and Horacio "El Negro" Hernandez splitting the drum chair six tracks apiece and Seamus Blake on four. Two more quickly followed, Historia (Fresh Sound New Talent, 2005), a trio with Ben Street and Antonio Sanchez plus Blake as guest, and Melancolía (Mavo, March 2006), which set the same band alongside a string quartet and added Luisito Quintero on percussion.

Vientos (Anzic Records, 2007) took the chamber idea further and became the record that fixed his reputation. A working quartet of Valera on piano and Fender Rhodes, Joel Frahm on tenor and soprano saxophones, James Genus on bass and Ernesto Simpson on drums plays all twelve pieces; on seven of them (tracks 1, 2, 5, 7, 8, 11 and 12) a five-piece woodwind ensemble joins, with Anat Cohen on clarinet, Anne Drummond on flute and alto flute, Aaron Heick on oboe and English horn, Michael Rabinowitz on bassoon and Charles Pillow on bass clarinet, adding English horn on track 8. Reviewing it for All About Jazz in July 2007, Jim Santella noted that Valera had swapped the French horn of the classical wind quintet for a bass clarinet, and heard tango, mambo and rhapsody folded into the swing. Currents (MAXJAZZ, 2009), a trio with Genus and Simpson, worked the standard repertoire on the same terms.

The Cuban side of the writing surfaced next. New Cuban Express (Mavo, June 2012) named the band that has carried it ever since, a sextet with Yosvany Terry on saxophones and chekeré, Tom Guarna on guitar, John Benitez on bass, Eric Doob on drums and Mauricio Herrera on percussion, drawing on the Cuban experimental groups of the 1970s and 1980s (Irakere, AfroCuba, Emiliano Salvador) rather than on the Latin-jazz mainstream. It was nominated for Best Latin Jazz Album at the 55th Grammy Awards in February 2013, in a field won by the Clare Fischer Latin Jazz Big Band's ¡Ritmo!. The band recorded Expectativas (2013), on which his father guests on a reading of José Antonio Méndez's "La Gloria Eres Tú," and In Motion (Criss Cross Jazz, 2014), cut in a single day at Systems Two in Brooklyn with Alex Sipiagin added on trumpet. Alongside it he made his first solo piano record, Self Portrait (2014), and a fusion date, Urban Landscape (Destiny, 2015), under the name Groove Square, with John Ellis, Nir Felder, Grégoire Maret on two tracks and the drum chair split between E.J. Strickland and Jeff "Tain" Watts.

A trio with Hans Glawischnig and E.J. Strickland ran through the second half of the decade and produced three albums: Live at Firehouse 12, taped in New Haven on October 10, 2014, The Seasons (2017) and The Planets (2018), the last of them written on a Chamber Music America and Doris Duke New Jazz Works commission. Chamber Music America has commissioned him three times, and he has twice taken awards from the Dranoff International 2 Piano Foundation. In 2019 he received a Guggenheim Fellowship in music composition, and began writing a song cycle on nine poems from José Martí's Versos Sencillos of 1891. His wife Lisa died of cancer while he was writing it. The result, José Martí en Nueva York (Greenleaf Music, August 2020), is the debut of the New Cuban Express Big Band, a big band with Camila Meza and Sofía Rei singing the texts; Distancia followed in March 2022 from the same band, assembled from sessions in December 2019 and October 2020.

He has kept three formats running in parallel since. The trio reappeared with Clarence Penn on Live at Diese Onze, recorded in Montreal in April 2019 and released in 2021, and again as a plugged-in trio with Janek Gwizdala and Mark Whitfield Jr. on Nevermind Tomorrow (2024). Vessel (Criss Cross Jazz, 2023) is a quintet date with Alex Norris, John Ellis, Hamish Smith and Whitfield. The New Cuban Express returned with Rise Again Vol. 1 (2024), written during the pandemic months when the band was rehearsing weekly before masked audiences at Terraza 7 in Queens, and Rise Again Vol. 2 (2025). Since 2020 he has also held the piano chair in Vital Information, the band the drummer Steve Smith has led since 1977, which Smith reconstituted as a trio with Valera and Gwizdala at the 2020 Drumeo Festival; that group has made Time Flies (2023) and New Perspective (2025). He is on the adjunct faculty of the Jazz Studies program at New York University's Steinhardt School.

Valera writes from two directions at once and has said the point is to make complex music that is simple on the ear. On one side is Havana, both the popular and the folkloric music, which shows in the clave-derived metric games and the danzón and bolero forms that keep reappearing in his large-ensemble writing; on the other is a conservatory ear for Ravel and Debussy, and, in the chamber records, for Stravinsky and Shostakovich. What ties them is voicing: he tends to write the harmony as color rather than as a chord sequence, which is why a woodwind quintet on Vientos and a string quartet on Melancolía sound like extensions of the piano rather than decoration. Reviewers have reached repeatedly for Chick Corea as a comparison, and Dan Bilawsky's 2012 notice of New Cuban Express conceded the resemblance while arguing it accounts for only a small part of the sound. His own list of influences runs to Herbie Hancock and Wayne Shorter for the jazz vocabulary and, for the big-band writing, to Thad Jones, Bob Brookmeyer, Kenny Wheeler and Carlos Franzetti. JazzTimes, reviewing José Martí en Nueva York, heard the Thad Jones and Mel Lewis band's swing and Wheeler's tone poetry in the orchestrations. As a pianist he is more architect than showman: the solos are built, the accompaniment is dense with countermelody, and the electric keyboards are used as an orchestration choice rather than as a fusion gesture.