Mathias Spahlinger was born in 1944 in Frankfurt. At the age of six, his father, a cellist, taught him the recorder, then the viola da gamba, and finally the cello. In 1952, Spahlinger also started taking piano lessons. In 1959, he developed an intense interest in jazz and took up the saxophone, going on to perform as an improviser in his hometown.

Upon leaving school in 1962, Spahlinger began an apprenticeship as a typesetter, and in 1965, started taking private composition lessons with Konrad Lechner. After completing his apprenticeship, he continued studying with Lechner at the Darmstadt Städtische Akademie für Tonkunst, where he also studied piano with Werner Hoppstock.

In 1968, he became a teacher at the Stuttgart Musikschule, and undertook further composition studies with Erhard Karkoschka at the Stuttgart University of Music and Performing Arts (HMDK) from 1973 to 1977.

In 1978, he was a guest lecturer of music theory at the Berlin University of the Arts, and in 1984 became a Professor of Composition and Music Theory at the Karlsruhe Hochschule für Musik. From 1990 to 2009, he was Professor of Composition and Head of the Institute for New Music at the Freiburg Hochschule für Musik.