Juan Bautista de Anza remained as governor of Nuevo Mexico (New Mexico) until 1787 when he returned to Sonora. He was appointed commander of the Presidio of Tucson in 1788 but died before he could depart and take office. Anza was survived by his wife.
Juan Bautista de Anza died in Arizpe, in what is now the State of Sonora, Mexico, and was buried in the Church of Nuestra Señora de la Asunción de Arizpe. In 1963, with the participation of delegations from the University of California, Berkeley and San Francisco, he was disinterred and reburied in a new marble memorial mausoleum at the same Church