The shooting was reported at Immaculate Heart of Mary Church near McFadden Avenue and S. Center Street, according to the Santa Ana Police Department.
Police say officers responded to a report about a fight in the parking lot. As officers arrived in the area, a parishioner alerted a passing officer that there was a man with a gun inside the church.
The officer-involved shooting happened when the officer entered the church and was confronted by the man.
"They did in fact come across a male adult who was armed with a gun," said SAPD Chief David Valentin. "An officer-involved shooting occurred inside the church near the altar."
The suspect ran out of the church and collapsed outside where he was pronounced dead. Police said he was found with a handgun.
Police said a small group was inside the church but services were not in progress. A witness captured video the moment police shot and killed the man.
"There had just been a gunshot when we were coming in," said church member Rita Orozco. "A lot of people were running. Police were running, there were guns, there were rifles, there were people crying."
No other injuries were reported.
Police say when officers initially responded to the scene, there were reports of a possible second gunman and shots fired, prompting officers to block access to several buildings on the church campus and search the area. No other suspects were found or evidence of another shooting.
There were only about a dozen worshipers inside the sanctuary at the time of the incident.
"This was not a mass casualty-intended incident," Valentin said. "Thankfully, by the grace of God, this incident also occurred in between mass services."
Investigators say the suspect was distraught and potentially suicidal when confronted by the officers.
The identity of the suspect was not known.
Police have not said if the suspect fired any gunshots.
No officers or church members were injured.