The federal indictment handed down on Thursday charged self-proclaimed white racist Payton Gendron, 19, on 14 hate crimes violations and 13 firearms offenses.
He also faces 10 counts of first-degree murder and 10 counts of second-degree murder in state court.
Authorities said he targeted the store because it was a hub in the predominantly Black tight-knit neighborhood.
The indictment came less than an hour before community members planned to gather at the Tops Friendly Markets store - the site of the shooting - for a moment of silence and prayer to commemorate the two-month anniversary of the May 14 attack.
The store, which has since been fully renovated, is set to reopen on Friday.
Buffalo Mayor Byron Brown said the Tops store reopening was a step forward in the community's efforts to heal.
"It is important to move forward as a united and strong community. We will not let hate win," he said.
Authorities say Gendron deliberately chose a place in a highly Black community in order to create as many Black casualties as possible.
His indictment on U.S. federal hate crimes charges was expected.