The incident was reported by multiple 911 callers shortly after 1 a.m. Saturday at the First Works Baptist church at 2600 Tyler Avenue, according to police.
"It appeared that the walls to the church had been vandalized as well as all the windows," El Monte police Lt. Christopher Cano said. The windows "appeared at first to be smashed, then we realized that the windows were not smashed, that they had actually blown out from some type of explosion," the lieutenant said.
No injuries were reported. Officials didn't immediately release details on the extent of the damage inside the building.
FBI technicians are working with the Los Angeles County Sheriff's Department bomb squad and the El Monte Police Department during the initial investigation, FBI spokeswoman Laura Eimiller said.
She said it was premature to call the incident a hate crime, but "that's always going to be considered as a theory when a house of worship is attacked."
"Although we do not yet know the motive, I am aware of the anti-LGBTQ+ and misogynist sermons given by the pastor of First Works Baptist Church," L.A. County Supervisor Hilda Solis said in a statement, "and my office has referred concerning matters pertaining to the pastor to the County's Human Rights Commission, who has been working in collaboration with the City of El Monte to de-escalate the situation."
El Monte Mayor Jessica Ancona called the incident "highly concerning" and said she was asking for a full and thorough investigation.
Protestors have repeatedly targeted the church headed by Pastor Bruce Mejia, who has condemned same-sex relationships.
A statement on its website says: "We believe that homosexuality is a sin and an abomination which God punishes with the death penalty."
Mejia's sermons and the church's stance were called hate speech during public comments at an El Monte City Council meeting, according to the Mercury News.
The Southern Poverty Law Center, a nonprofit advocacy organization specializing in civil rights litigation, listed the church on its 2019 watch list of "anti-LBGTQ hate groups."
An online petition by a group called Keep El Monte Friendly that calls for the church to be kicked out of the city had more than 15,000 signatures as of Sunday morning.
Eyewitness News reached out to the church for comment but the request has not been answered.
Anyone with information about the explosion is urged to contact the FBI's Los Angeles field office at (310) 477-6565 or www.fbi.gov/tips.
The Associated Press contributed to this report.