Eddy Louiss was born Alain Édouard Louise on May 2, 1941, in the 14th arrondissement of Paris, into a family of musicians. His father, Pierre Louiss (1908-1986), was a trumpeter from La Trinité, Martinique, who had altered the spelling of the family name from Louise; Eddy grew up playing in his father's orchestra as a teenager and studied trumpet, piano, and organ. In the early 1960s he worked as a pianist in Paris nightclubs while continuing his studies, and in 1961 he joined the vocal group Les Double Six, singing alongside founder Mimi Perrin, Roger Guérin, Ward Swingle, and Christiane Legrand, sister of the composer Michel Legrand. It was during his three years with Les Double Six that his primary instrument shifted to the Hammond organ, and in 1964 he won the Prix Django Reinhardt of the Académie du Jazz.

Through the rest of the 1960s Louiss built a busy career as an organist, recording and performing with Johnny Griffin, Art Taylor, Dizzy Gillespie, and Stan Getz, and joining drummer Kenny Clarke's trio alongside guitarist René Thomas. In 1968 he recorded the live trio album Trio HLP at the Paris club Le Caméléon with violinist Jean-Luc Ponty and drummer Daniel Humair, and cut his own first Barclay leader date (arranged with trumpeter Ivan Jullien) the same year. In August 1970 he traveled to Tokyo to record Our Kind of Sabi, a co-led trio session with British reedman John Surman and Humair, made for a Japanese tour of European Down Beat poll winners and produced by the German critic Joachim Ernst Berendt. The following year he joined Stan Getz's touring European quartet, with René Thomas and drummer Bernard Lubat, documented on the celebrated live double album Dynasty, recorded at Ronnie Scott's in London and released on Verve in 1971. He also cut two solo organ-trio albums of his own, Orgue and Orgue Vol. 2 (1972, America Records), with guitarist Jimmy Gourley, bassist Guy Pedersen, and Clarke, and co-led a big-band recording of Porgy and Bess with Jullien the same year.

In November 1972 Louiss recorded the first of several studio collaborations with violinist Stéphane Grappelli, released in 1974 as Satin Doll; further duo and small-group sessions followed later in the decade, including recordings of Cole Porter and Gershwin songbooks, and a separate, undated Grappelli-Louiss session was reissued in 1993 as Blue Skies. Alongside his jazz work, Louiss spent roughly thirteen years, from 1964 to 1977, as musical director and organist for the singer Claude Nougaro, and also recorded and toured behind Jane Birkin and Henri Salvador. By the 1980s he had formed his own big band, Multicolor Feeling, which toured extensively across Europe and appeared on record as the Multicolor Feeling Fanfare beginning in 1989. His 1987 album Sang Mêlé included the blues "Blues for Klook," dedicated to Kenny Clarke's nickname, which later became widely used as competition music by figure skaters and gymnasts.

The most celebrated recordings of Louiss's later career were made in duo with pianist Michel Petrucciani: Conférence de Presse (1994) and Conférence de Presse Vol. 2 (1995), both for Dreyfus Jazz, won the Victoires du Jazz award for instrumental jazz album of the year in 1995. He went on to record the duo album Face to Face (2001) with accordionist Richard Galliano, and led further sessions including Louissiana (1995), recorded with New Orleans musicians including bassist George Porter Jr., and Récit Proche (2001). In 2004 and 2005 he recorded and performed tribute concerts to Nougaro, Ô Toulouse... Hommage à Claude, with Bernard Lubat and other longtime collaborators. Diabetes-related arterial complications forced the amputation of his left foot in 2006, not long after a performance at the Jazz in Marciac festival that August, and a long rehabilitation followed; he nonetheless returned to the stage, and in 2010 marked fifty years in music with a concert at the Paris Olympia featuring a revived, sixty-plus-musician Multicolor Feeling Fanfare, the same year he recorded the album Taurorque.

In June 2015 Louiss underwent cataract surgery; a subsequent fall required a further operation, and he passed away during that procedure at the university hospital in Poitiers on June 30, 2015, at the age of seventy-four. His funeral was held on July 6, 2015.

Louiss belongs to the small group of European organists, alongside Jimmy Smith's American disciples, who established the Hammond B3 as a genuine jazz solo voice outside the United States; critics and obituarists routinely credit him as the most important French jazz organist of his generation. His playing combined a blues-and-groove foundation, audible in the organ-trio format he favored throughout his career, with a harmonic sophistication and lyricism that let him work as convincingly in a spare duo with a classically trained violinist (Stéphane Grappelli) as in the free-flowing two-piano-and-organ conversations he held with Michel Petrucciani. His earlier training as a vocalist with the vocalese group Les Double Six left a lasting mark: he continued to sing on his own later records, including WéBé, and his phrasing on the organ was often described as vocal in character. In the last two decades of his career his writing and arranging, on albums such as Sang Mêlé and Récit Proche, increasingly drew on his father's Martinique heritage and on electronic and rock textures alongside straight-ahead jazz.