A lawyer on Thursday entered the plea for Payton Gendron, 18, in the first case to make use of New York state's domestic terrorism hate crime law.
Gendron did not speak during the brief hearing with a heavy security presence.
Witnesses, police and Gendron's own writings and live-streamed video have incriminated him as the gunman who used an AR-style semi-automatic rifle on May 14 to target shoppers and employees of a Tops Friendly Market.
He surrendered at the crime scene after putting his rifle to his neck.
Authorities said he chose the store because it was in a predominantly black neighborhood.
"There is overwhelming proof of the defendant's guilt," Assistant District Attorney John Fereleto said.
"The defendant was caught at the scene of the crime with the weapon in his hands."
Gendron has been held without bail and is due back in court on July 7.
He was charged with murder shortly after the attack.
On Wednesday, a new indictment expanded the case to include the domestic terrorism charge, along with 10 counts of first-degree murder, 10 counts of second-degree murder as a hate crime, criminal possession of a weapon and three counts of attempted murder as a hate crime.
"When you hear the phase 'throw the book at' someone, well, in this case right here, the defendant just got War and Peace," District Attorney John Flynn said at a news conference after the arraignment.
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