He studied in Orlando, FL, and at Wheaton College in Illinois, then took conducting from Jean Morel at the Juilliard School in New York. While there, he won the Irving Berlin Award for conducting. He worked primarily in New York, in a variety of freelance jobs (including conducting on some of Peter Schickele's "P.D.Q. Bach" performances on the Vanguard Records label).
One of his notable accomplishments was organizing and conducting the New York concert premiere of the immense opera Les Troyens by Hector Berlioz, one of the composers he most deeply admires. He had already made his opera-conducting debut at the New York City Opera, in 1972, with Carmen. The success of his Troyens performance led to an immediate engagement to conduct it at the Metropolitan Opera in New York, in 1973. He also conducted the American premiere of Benjamin Britten's Owen Wingrave at Santa Fe.
In 1976, he was appointed music director of the Indianapolis Symphony Orchestra. During his tenure there, the orchestra became a full-time (52 weeks a year) organization. Nelson returned the orchestra to recording (on the New World label) and led its move to the intimate Circle Theater (now Hilbert Circle Theater) in the city's center. He is credited with improving the orchestra's ensemble and sound.
In 1979, he also became associated with the Opera Theater of Saint Louis, and in 1983 was appointed music director of the Caramoor Festival. After a dangerous illness in the mid-'80s, he gave up all these positions (in 1987, 1991, and 1990, respectively) and transferred his major activities to Europe, where he gained a reputation as a major operatic conductor, especially following a highly praised recording of Benvenuto Cellini in Lyons, in 1989.
He has conducted many of the leading symphony orchestras of the world, including the Los Angeles Philharmonic, the Saint Louis, Chicago, Pittsburgh, Boston, and San Francisco Symphonies, the Cleveland Orchestra, the Dresden Staatskapelle, the Leipzig Gewandhaus, Orchestre de Paris, the Oslo Philharmonic, and the orchestras of Stockholm, Rotterdam, Stuttgart, and Cologne. As an opera conductor, he has appeared at the Chicago Lyric Opera and the opera houses of Rome, Geneva, and Paris. His operatic repertory is wide, ranging from Handel to contemporary opera. In the concert hall, he conducts the great choral masterworks of Bach, as well as new works, including Takemitsu's I Hear the Water Dreaming, and Paul Schoenfeld's Deborah, which he premiered. John Nelson has recorded frequently, including acclaimed recordings of Berlioz's Beatrice et Benedict, and Handel's Semele (a Grammy award winner). He has formed an organization to raise money and commission new major sacred choral-orchestral works, redressing, he says, the secular emphasis of twentieth-century music. Schoenfeld, Henryck Gorecki, Christopher Rouse, Oswaldo Golijov, and Augusta Reed Thomas are among the composers the organization, Soli Deo Gloria Inc., has commissioned.
In 1998, he accepted the position of music director of the Ensemble Orchestral de Paris, a 14-week a year commitment that will enable him to pursue his operatic and other conducting projects.