Born to a lyric singer father and a pianist mother (Clarisse Leite), Baptista studied classical piano from 1955 to 1959, double bass from 1962 to 1963, and acoustic guitar from 1963 to 1965. In 1966 he formed the influential Os Mutantes band with his brother Sérgio Dias and Rita Lee, where he played bass guitar, keyboards and sang. Baptista left the band in 1973 due to disagreements with the other members of the band and the excessive use of LSD. In 1974 he tried to work as a musical producer, with no success. This motivated him to try a solo career, and in the same year, he released the album Lóki?, which is considered his best work.

Baptista recorded two albums with the band Patrulha do Espaço between 1977 and 1978, and later resumed his solo career. In 2006, Os Mutantes reunited without Rita Lee, and Baptista played with his brother Sérgio and the drummer Dinho Leme 33 years after originally leaving the band. In 2007 Baptista left the band again to pursue personal projects.