San Diego County prosecutors also charged John T. Earnest on Monday with an earlier arson attack on a mosque in Escondido about March 23.
The murder and attempted murder charges stemming from Saturday's shooting at Chabad of Poway - with a congregant slain and a rabbi, another man and a girl wounded - carry special-circumstance allegations of a hate crime.
The District Attorney's Office said in a statement that Earnest will be arraigned Tuesday afternoon.
The accused gunman appears to be the author of an online manifesto and drew inspiration from last month's mass shooting at two mosques in Christchurch, New Zealand that killed 50 people.
On Monday, California lawmakers adopted a resolution in honour of Holocaust Memorial Day and took a moment during a ceremony to speak about the attack.
Assemblyman Jesse Gabriel, vice chairman of the California Legislative Jewish Caucus, said the state's Jewish community is alarmed by the "infusion of anti-Semitism into our political discourse."
He emphasised that the Holocaust "didn't happen overnight" and that people should be aware of smaller deeds such as hateful rhetoric.
The FBI said it got tips about a threatening social media post about five minutes before the attack but it was too late to identify the suspect.
