Carlos Caires graduated in Composition from the Escola Superior de Música de Lisboa (Composition with Constança Capdeville and Christopher Bochmann) and went on to obtain a Maîtrise (1999), a Diplome d'Études Approfondies (2000) and a PhD (with an FCT scholarship, 2006) from the University of Paris8 Saint Denis-Vincennes, under the guidance of Horacio Vaggione. He is a coordinating professor at the Escola Superior de Musica de Lisboa, where he began teaching in 1993, a researcher at CITAR-Universidade Católica (Porto) between 2007 and 2013, and an integrated researcher at CESEM-FCSH since 2014. He is also a collaborator at the CICM-Centre de recherche Informatique et Création Musicale (University of Paris8, Saint-Denis Vincennes).

He was a teacher at the Setúbal Regional Conservatory and at the Music School of the National Conservatory (between 1988 and 1991). Alongside his composition course, Carlos Caires attended various summer courses in choral and orchestral conducting in Portugal and abroad. Together with conductor Paulo Lourenço, he directed the choir of the Portuguese Musical Youth, later founding (also with Paulo Lourenço) the Ricercare Choir, which he directed until 1998, when he left for Paris.

His music has been performed at various festivals in Europe, Asia and the USA.

Among the ensembles that have performed his music are the Casa da Música Symphony Orchestra, the Casa da Música Choir, the Remix Ensemble, the Gulbenkian Orchestra, the Lisbon Metropolitan Orchestra, the Portuguese Symphony Orchestra, the Symphony Orchestra and the Lisbon School of Music Wind Orchestra, Chamber Choir of the Lisbon School of Music, Wind Orchestra of the University of Aveiro, OrchestrUtopica, Coro Ricercare, Sinfonietta de Lisboa, Lisbon Contemporary Music Group, Ensemble Ars Ad Hoc, Ensemble Futurs Musiques, Gruppo di Percussione d'ella RAI, Sond'Ar-Te Electric Ensemble and Smith Quartet.

In 1995 he was awarded the Joly Braga Santos Prize for his work Al Niente, in 1996 the Claudio Carneyro Prize for his work Wordpainting, and in 1998 the ACARTE Prize for his work Retábulo-Melodrama. Carlos Caires has developed various computer applications in the fields of electroacoustic music and computer-assisted composition, most notably the sound micromontage software IRIN, a project he began during his doctorate and has been updating to this day.

His work also includes composing music and sound for film, and he has so far presented four animated short films at the Monstra Festival, which were later shown internationally.