 De Bono died in Valencia on 14 July 1604, at the age of 74.His remains were first entombed in the Church of San Sebastián, to which the monastery was attached.After the suppression of the monastery under the Napoleonic rule of Spain, the urn containing his bones was moved in 1835 to the Church of San Nicolás, where he had been baptized as a baby, and enshrined under the altar of the Chapel of St. Raphael.