Emmanuel Nunes was born in 1941 in Lisbon where he studied harmony and counterpoint between 1959 and 1963 in the Academy of Music with Francine Benoît. From 1961 to 1963, he followed courses of Germanic philology and Greek philosophy in the University of Lisbon. He undertook summer courses in Darmstadt (1963 to 1965), where he was particularly marked by the courses of composition of Henri Pousseur and Pierre Boulez. The analysis of Momente, by Stockhausen, is seen by Nunes as the most significant stage of his first initiation to composition.

He teached composition, since 1981, at the Calouste Gulbenkian Foundation in Lisbon, and, from 1986 to 1992, he also taught at the Musikhochschule of Freiburg-im-Breisgau. Emmanuel Nunes was nominated professor of composition at the Conservatoire National Superieur de Musique et de Danse de Paris in 1992. He also pursued his teaching activities at Harvard University, at IRCAM, at the Darmstadt summer courses and at ICONS (Novara, Italy).