Amat arrived in the pueblo of Los Angeles in 1855. On July 7, 1859, the diocese was renamed the Diocese of Monterey-Los Angeles. The Co-Cathedral of Saint Vibiana was founded in Los Angeles and consecrated during the episcopacy of Amat. He brought back from Rome the relics of its patron saint, which were interred in a sarcophagus above the cathedral's main altar.
Father Amat traveled to Rome in 1869 to attend the First Vatican Council called upon by Pope Pius IX. On June 28, 1870, Father Amat was an orator during the official mass of the 78th Congregation celebrated in the Vatican.
Amat came into conflict with Friar José González Rubio, O.F.M., of the Mission Santa Barbara, over the control of the mission after President Abraham Lincoln returned the California missions to the Catholic Church. The Franciscans claimed, on the basis of both Church law and historical grounds, that the missions were rightfully under their direct jurisdiction and not that of the diocese. Accordingly they claimed that they should hold the deed to Mission Santa Barbara.[citation needed]
Amat died on May 12, 1878, at Los Angeles, California, and was succeeded by his coadjutor bishop, Francisco Mora y Borrell, who (like Alemany and Amat) was also Catalan. He was originally buried in the crypt of the co-cathedral in Los Angeles, but, due to earthquake damage, is now buried in the bishop's crypt of the Cathedral of Our Lady of the Angels, which replaced it in 2002.