Following a 2002 report from a task force appointed by Roger Mahony, the Archdiocese of Los Angeles closed the undergraduate portion of the seminary.

The task force also scheduled a 2005 review to see if St. John's should be entirely closed with Loyola Marymount University taking over the school's functions; this shutdown has not come to pass.

[13] Alumni of St. John were accused in the sexual abuse scandal, which broke into public in the late 20th century, of molesting underaged boys and young men.

Of the approximately 625 St. John's graduates to be ordained by the Los Angeles Archdiocese between 1950 and 2005, by 2005 65 had been accused in the sexual abuse scandal, reflecting a rate higher than what studies have found for U.S. priests in general.

A seminary spokesman noted in November 2005 that California had extended its statute of limitations on molestation lawsuits, making more cases possible for prosecution.