The Chaldean Catholic Church is an Eastern Catholic church in full communion with Rome, using the East Syriac liturgical rite and tracing its origins to the ancient Christian communities of Mesopotamia. Chaldean Catholics have been present in what is now Iraq for nearly two millennia. The community in El Cajon developed over decades as Chaldean and Assyrian immigrants settled in the broad valley east of San Diego, drawn by established networks, affordable housing, and the presence of the community that had preceded them. El Cajon now has one of the largest concentrations of Assyrian and Chaldean people outside the Middle East. The cathedral is the institutional center of that community's religious life.

The parish of St. Peter was established in 1973 with Father Peter Kattoula as its first pastor. A decade later, the congregation had grown enough to build a permanent church, completed and dedicated on September 10, 1983, seating 600 people. The parish's growth reflected the growth of the Chaldean community in El Cajon through the 1970s and 1980s. When the Vatican established the Eparchy of St. Peter the Apostle in 2002 — the first Chaldean Catholic diocese established in the United States specifically to serve the West Coast Chaldean community — the existing church in El Cajon became the cathedral, the bishop's seat. The eparchy covers the western United States and Alaska.

In September 2020, the cathedral was vandalized with contradictory graffiti — messages that targeted the cathedral from multiple ideological directions simultaneously, suggesting opportunistic rather than ideologically coherent vandalism. The incident prompted law enforcement attention and community response. Vandalism targeting religious sites follows a particular pattern: the act damages a community's sense of safety and belonging, the response typically involves both practical repair and public solidarity. The cathedral's position as the visible center of the Chaldean community in El Cajon made it a notable target, whatever the motivations of the individuals involved.

The $650,000 raised in 2014 for Christian refugees from Mosul and the Nineveh Plains represents the cathedral functioning as what cathedrals have functioned as throughout history: a point of organized communal response to crisis. The Chaldean community in El Cajon had personal connections to the people being displaced — families, former neighbors, members of the same ancient church tradition being driven from lands their ancestors had occupied since before the Arab conquest. The fundraising was not abstract charity but an expression of kinship across an ocean and a centuries-old displacement that had just become acute again. The cathedral held the community together for that response, as it does for ordinary Sundays and feast days and the accumulated life of a diaspora far from home.