Gendron, from the town of Conklin, New York, was arraigned in a Buffalo court on one count of murder in the first degree, said Erie County District Attorney's Office.
Gendron appeared in the court for less than five minutes and pleaded not guilty, according to a report by United Press International.
The shooter was remanded without bail, and a felony hearing is scheduled for Thursday, according to Erie County District Attorney's office.
"This defendant is accused of traveling to our area and targeting innocent people who were shopping for their groceries on a Saturday afternoon ... My office is working closely with the U.S. Attorney's Office and our partners in law enforcement into potential terrorism and hate crimes. This is an active investigation and additional charges may be filed," said Erie County District Attorney John Flynn in a statement.
If convicted, Gendron faces a maximum sentence of life in prison without parole, added Flynn.
U.S. Attorney General Merrick Garland said in a statement that the Department of Justice "is investigating this matter as a hate crime and an act of racially-motivated violent extremism."
Garland vowed to conduct "a thorough and expeditious investigation into this shooting" and seek "justice for these innocent victims."
Meanwhile, attention quickly turned to fundamental issues like white supremacism, social media and gun violence.
"A racially motivated hate crime is abhorrent to the very fabric of this nation. Any act of domestic terrorism, including an act perpetrated in the name of a repugnant white nationalist ideology, is antithetical to everything we stand for in America," said U.S. President Joe Biden in a statement.
Biden called for the elimination of hate crime and hate-fueled domestic terrorism.
"We'll be aggressive in our pursuit of anyone who subscribes to the ideals professed by other white supremacists and how there's a feeding frenzy on social media platforms where hate festers more hate, that has to stop," said New York Governor Kathy Hochul in a press conference on Saturday evening.
"We must do more to address the scourge of racism and anti-Semitism, and to pass commonsense gun safety measures to keep our communities safe," said U.S. Senator Kirsten Gillibrand from New York State.
Hochul urged social media platforms to be vigilant in monitoring content and pushed for legal responsibility to ensure that such hate cannot populate social media sites.
The gunman live-streamed the shooting on Twitch, a platform best known for gaming, and posted a racist and anti-Semitic manifesto online, according to reports.
Twitch was quick to respond saying it has a "zero-tolerance policy against violence of any kind and works swiftly to respond to all incidents. The user has been indefinitely suspended from our service, and we are taking all appropriate action, including monitoring for any accounts rebroadcasting this content."
The suspect is believed to have used a gun that was legally purchased but modified with illegal magazines, according to Hochul.
"I've seen violence from guns on the Brooklyn subway, and now in the streets of Buffalo, it has to stop," said Hochul.
According to a database run by the nonprofit research group Gun Violence Archive, more than 28,000 people have died or been injured due to gun-related incidents in the United States this year.