Mr Gendron allegedly killed 10 people in a mass shooting at a grocery store in Buffalo, New York in May.
He was indicted last week by a federal grand jury on more than two dozen charges, including 10 counts of hate crimes resulting in deaths, three counts of hate crimes involving an attempt to kill and 13 counts of using, carrying, or discharging a firearm in relation to a hate crime.
Mr Gendron, who is white, drove to a Tops Supermarket in a predominantly Black neighborhood in Buffalo on 14 May where he began shooting shoppers.
He surrendered to police officers responding to the shooting.
According to Fox News, Mr Gendron appeared in an orange prison jumpsuit wearing shackles for his plea hearing on Monday.
Mr Gendron did not speak. His attorney entered his plea and said that his client could enter into a plea agreement before a trial begins.
Also in the courtroom were family members of the victims, including Zeneta Everhart, whose son Zaire Goodman was wounded during the mass shooting.
She said she is hoping Mr Gendron goes to prison for life but would support the death penalty if prosecutors seek that punishment.
"It's hard," she said after the hearing. "My son is still recovering from gunshot wounds. It's hard sitting in that courtroom with a terrorist."
New York Governor Kathy Hochul called the shooting an act of "white supremacy terrorism," and at the time urged social media companies to do more to combat extremism on their platforms.
"I'm calling on social media platforms to be making sure that they're doing a better job monitoring the hate speech that's out there, especially when it's directed against populations and comes under the guise of white supremacy terrorism, which is exactly what happened here in Buffalo," Ms Hochul said during an interview with "Face the Nation." She was referencing the shooter’s white nationalist manifesto which was shared on social media ahead of the attack.
Mr Gendron initially streamed his attack on the social media streaming platform Twitch before the feed was removed. Twitch said it managed to take down the stream two minutes after the attack began.
Ms Hochul said at the time that better monitoring was needed to prevent further incidents.
“This information was out there. This was on a manifesto that was written a while back and so we’re very concerned about what other information is perpetrated out there on social media platforms and are out there being disseminated globally,” she said. “This information from yesterday’s attack is already out there, it was live-streamed, the intent of this individual was telegraphed in advance.”
Mr Gendron's next status hearing will be 9 December. He was then returned to state custody.