He was one of the leading figures in the musically progressive Ferrara school in the late 16th century, and one of the earliest composers in the seconda pratica style at the transition to the Baroque era.
It was in the employ of the Este family that he first went to Rome in 1586; while there he probably met the renowned madrigalist Luca Marenzio, as well as members of the Roman school of composition, aspects of whose style appear in his music.
He found refuge with the opulent Roman household of Cardinal Alessandro d'Este, the younger brother of Duke Cesare who had banished him from Modena, and continued his musical life in Rome.
During the next ten years he traveled widely, including a stay in Florence to try to mediate conflicts among the Medici court musicians, and a sojourn in Spain in 1611 and 1612 as the Este representative.
Gustave Reese, in his encyclopedic Music of the Renaissance, never mentions him, yet Alfred Einstein, in his comprehensive The Italian Madrigal, praised him as being the finest of the nobleman-composers at the end of the 16th century, a category that would include Gesualdo as well as Alessandro Striggio.
Like Gesualdo and Luzzaschi, Fontanelli wrote madrigals which were intended to be appreciated by a small audience of connoisseurs, particularly the musica secreta of Alfonso II d'Este.
None are obviously intended for arrangement for solo voice and accompaniment by a plucked chordal instrument (as are many of Luzzaschi's madrigals), being contrapuntal and disjunct in texture, and avoiding a dominant soprano line.