 De Bono was born on 5 January 1530 in Valencia, the second of the four children of Juan de Bonom (or Joan de Bonome), who had emigrated from Gascony, and his wife, Isabel Juana Manzón (or Monzon), originally from Villa de Cervera in the Province of Lleida ().Upon his birth, he was baptized at the nearby Church of San Nicolás.Having been born on the eve of the Feast of the Epiphany, he was named for one of the Biblical Magi.