[7] After his ordination, the diocese assigned Cordileone as an associate pastor at Saint Martin of Tours Parish in La Mesa, California, until 1985.

[6] Back in San Diego he was appointed as priest secretary to Bishop Robert Brom and a tribunal judge (1989–1990), adjutant judicial vicar (1990–1991), and pastor of Our Lady of Guadalupe Parish in Calexico, California (1991–1995).

In September 2009, Cordileone offered a pontifical high mass (in Latin, missa pontificalis) at Saint Margaret Mary Church in Oakland.

[18][20] In a June 2012 EWTN News interview, Cordileone stated that redefining marriage to include LGBTQ couples would be bad for children, detrimental to society and dangerous for religious freedom.

Shortly before his installation as archbishop, on August 26, 2012, Cordileone was arrested for driving under the influence of alcohol at a police checkpoint in San Diego.

The court also required him to attend a Mothers Against Drunk Driving victim-impact panel and participated in a three-month first conviction program through the California Department of Motor Vehicles.

[29] In February 2015, Cordileone told archdiocesan school teachers that they were expected to conduct their public lives in a way that did not undermine or deny Catholic doctrine.

[30] Ting and Mulin then called for an investigation of working conditions at archdiocesan high schools over the archbishop's proposed morality clauses for teachers.

[32] In April 2015, over 100 Catholic donors and church members from the Bay Area signed a full-page advertisement in the San Francisco Chronicle, appealing to Pope Francis to replace Cordileone as archbishop.

The ad specifically objected to Cordileone's characterization of extramarital sex and LGBTQ relationships as "gravely evil", saying that he fostered "...an atmosphere of division and intolerance".

This document opposed same-sex marriage, abortion rights and assisted suicide, and condemned what the signers believed was an infringement on freedom of religion.

[citation needed] In an interview with USA Today in March 2013, Cordileone discussed the US Supreme Court's then-pending decision on the constitutionality of Proposition 8.

Before the March, at least 80 religious leaders, lawmakers and officials (including the mayor of San Francisco) collected a petition with 30,000 signatures, urging him not to attend it.

They specifically objected to Cordileone "marching and sharing the podium with individuals who have repeatedly denigrated lesbian, gay, bisexual, and transgender people."

[45] In June 2014, Cordileone and several other bishops criticized the reported intention of US President Barack Obama to issue an executive order on LGBTQ employment.

[50]"In April 2022, Cordileone warned Pelosi, a Catholic resident of San Francisco, that he would prohibit her from receiving the eucharist within the archdiocese unless she repudiated her support of abortion rights for women.

He stated, "A Catholic legislator who supported procured abortion, after knowing the teaching of the Church, commits a manifestly grave sin which is a cause of most serious scandal to others."

[51][52] Cordileone's action against Pelosi came following the May 2022 Supreme Court leak suggesting that it might overturn its 1973 Roe v. Wade decision legalizing abortion nationwide.