Giovanelli composed and published a large number of secular pieces. He is noted for his church music, most of which also survives in manuscript. As could be expected for a composer of the Roman School, his sacred music was conservative, and mostly in the Palestrina style for the first part of his career; however, after 1600 he experimented with some of the stylistic innovations which defined the beginning of the Baroque era, such as the "concertato" principle and the "basso continuo." His output of sacred music fell off dramatically late in his life, and at least one scholar has suggested that this was because he was uncomfortable with the new style. In 1615 he created a new edition of the "Graduale" known as the "Medicean", published by the Medici press. ("The Encyclopedia Americana" may contradict this, writing that a "Editio Medicæa of the Graduale" of 1614 was created by Felice Anerio.)