San Diego County prosecutors also charged John T. Earnest on Monday with an earlier arson attack on a mosque.
The murder and attempted murder charges stemming from Saturday's shooting at Chabad of Poway carry special-circumstance allegations of a hate crime.
The District Attorney's Office says in a statement that Earnest will be arraigned Tuesday afternoon.
Congregation member Lori Gilbert Kaye, 60, of Poway was slain and a rabbi, another man and a girl were wounded in the attack.
The mosque fire occurred on or about March 23 in the city of Escondido.
A funeral service was held for Kaye in Poway. She was praised for her spirit of giving. It is believed she died while shielding the synagogue's rabbi and others from gunfire during the attack.
"You epitomized all that is light and good in the world," Kaye's sister said at the service. "I do know how we go on. We go on by emulating all you taught us, your positive attitude, to live life to the fullest."
Others wounded in the shooting were the congregation's rabbi, Yisroel Goldstein, while 8-year-old Noya Dahan and 34-year-old Almog Peretz suffered shrapnel wounds.
A vigil was held to honor Kaye at Poway High School at 6:30 p.m. More than 4,000 attended and were asked to wear blue to show solidarity for the victims.
Earnest's parents said their son and five siblings were raised in a family that "rejected hate and taught that love must be the motive for everything we do." They said they were shocked and mystified.
"Our son's actions were informed by people we do not know, and ideas we do not hold," the family said in its first public comments.
They said they were cooperating with investigators to help "uncover many details of the path that he took to this evil and despicable act." They do not plan to provide their son with legal representation, according to their attorney, Earll Potts. A public defender will likely be appointed.
The Associated Press contributed to this report.