During the 18th century, the San Bernardino and Riverside areas were part of the province of Las Californias in the Spanish colony of New Spain.

[6] The pope named Reverend Charles F. Buddy from the Diocese of Saint Joseph as the first bishop of San Diego.

Buddy was close friends with Auxiliary Bishop William O'Brien, director of the Catholic Church Extension Society of Chicago.

[9] To replace Furey in San Diego, Paul VI that same year appointed Bishop Leo Maher from the Diocese of Santa Rosa.

[11] He presided over the second diocesan synod from 1973 to 1976, revising the statutes and guidelines of the diocese to implement the reforms of the Second Vatican Council.

[12] He ended the official relationship between the diocese and the University of San Diego, establishing the school as a separate corporation.

[13] He also supported workers' rights to organize into unions, but pledged an official neutrality in a farm labor dispute in 1971.

[14] That same year, he suspended Reverend Victor Salandini, a San Diego priest and ally of labor organizer César Chávez, for wearing a serape with the black eagle symbol of the United Farm Workers instead of proper vestments and for using corn tortillas instead of sacramental bread during his masses.

A 16-year-old boy in 1977 filed a complaint of sexual assault against Reverend John Daly with the Holtville police.

The boy said that Daly picked up him and a companion while hitchhiking and offered to let them stay for the night at St. Joseph Church.

[23] Reverend Edward Rodrigue pleaded no contest in 1979 of sexually abusing an 11 year old developmentally disabled boy in Highland.

[25] Five women sued the diocese in 2003, claiming that they had been sexually assaulted as minors by Reverend Franz Robier during the 1950s.

Records showed that Bishop Buddy sent Robier away for treatment after receiving complaints, then allowed him later to resume ministry.

[31] In December 2018, Reverend Juan Garcia Castillo from St. Patrick Parish in Carlsbad was convicted of sexual battery.

[34] On December 11, 2019, it was announced that four victims of convicted, and now deceased, sexual abuser Anthony Edward Rodrigue would sue the Diocese of San Diego.

[38] In June 2024, the diocese announced that they would be preparing to file for Chapter 11 bankruptcy for a second time to settle with the hundreds of sex abuse lawsuits.