Robert Bowers, 46, spoke little in court on Thursday, other than to say he understood the charges against him and to enter a “not guilty” plea.
If convicted, Bowers could face the death penalty.
Authorities say Bowers raged against Jews during and after what is believed to be the deadliest anti-Semitic attack in US history.
Bowers, who was shot and wounded during a gun battle that injured four police officers, walked into court under his own power, his left arm heavily bandaged. He was in a wheelchair at his first court appearance on Monday.
The suspect frowned as the charges were read but did not appear to react as a federal prosecutor announced he could face a death sentence. He told a prosecutor he had read the indictment.
One of his federal public defenders, Michael Novara, said Bowers pleaded not guilty, “as is typical at this stage of the proceeding.”
Bowers had been set for a preliminary hearing on the evidence, but federal prosecutors instead took the case to a grand jury.
The panel issued the indictment as funerals continued for the victims.
Jared Younger of Los Angeles told mourners that he waited for hours on Saturday for his father to pick up his phone or let them know he was all right. The dread built all day until his sister learned their father, Irving Younger, had been shot and killed.
“That waiting stage was just unbearable,” Jared Younger said at his father’s funeral Wednesday. “Saturday was the most lonely day of my life.”