While he held these positions, he wrote and published a favola boscareccia entitled I fidi amanti (Verona, 1593) in anticipation of the wedding of Don Carlo Gesualdo and Eleonora d'Este which took place in Ferrara the following year (1594).
Upon the death of Bevilacqua, Pasquini apparently returned to Ferrara, where he succeeded Luzzasco Luzzaschi as organist of the Accademia della Morte.
Among the items which have come down to us are 6 toccatas, 2 durezze, 9 or 10 canzonas, 5 sets of variations, 3 dances, and an intabulation of Cipriano de Rore's madrigal Ancor che co'l partire.
The madrigal Mentre che la bell'Isse of 1591, appears as a contrafact motet Sanctus Sebastianus in a Passau collection.
A spiritual madrigal M'empio gli occhi di pianto, to a text by Angelo Grillo, appeared in 1604, and the final work, published after his death, is Jesu decus angelicum for four voices and organ.