Three men were killed, including a man who worked as a security guard at the mosque, in Monday's attack.
The suspects, a 17-year-old and an 18-year-old, were found dead in a car near the mosque during a police operation and are believed to have taken their own lives.
In addition to several firearms, police secured a manifesto during the searches, the AP news agency writes. The authorities did not want to specify the content, but said it concerned texts expressing hatred directed at several religions and groups.
“Early stage of the investigation”
The incident is being investigated as a hate crime, but it has not been determined whether the mosque was the main target.
"We are at too early a stage of the investigation to say that the San Diego Islamic Center was the specific target. We are evaluating and analyzing all the evidence," said Mark Remily of the FBI at a press conference on Tuesday, according to CNN.
"What I can say is that they definitely had a broad hatred for many people."
Earlier that morning, hours before the shooting, the mother of one of the teenagers contacted police with concerns. Her son was described as suicidal and had left home with a weapon.
A search operation was launched, but the police were unable to find him in time.
Children were escorted out
The mosque has its own school for students aged five and up. Many children were also there when the shooting broke out at lunchtime on Monday, but all were unharmed.
Both police and representatives of the mosque say the security guard who was shot dead prevented the shooters from advancing further into the buildings.
"He undoubtedly saved lives," Police Chief Scott Wahl said at a previous press conference.
