Wert first became ill with malaria in 1582, and ill-health was to bedevil him for the rest of his life. Even so, he remained musically productive, writing a coronation mass for Duke Vincenzo Gonzaga in 1587, and numerous madrigals for the "concerto delle donne", the renowned group of musical ladies of Ferrara, who were virtuoso singers. In 1592, Giovanni Giacomo Gastoldi took over his post as "maestro di cappella" in Mantua, and in August 1595 he dedicated his last book of madrigals. Wert died in 1596 in Mantua, in his house near the ducal palace; his tomb is near to that of his contemporary Francesco Rovigo, in the crypt of Santa Barbara, beneath the church where he worked for many years.