The self-avowed white supremacist entered the plea during an afternoon hearing. He stood at the defense table with his attorneys, clad in a gray and white striped jail jumpsuit and handcuffed to a chain at his waist.
Roof was unapologetic at his federal trial as he listened to days of testimony from survivors. They described in harrowing detail the hail of bullets that began when parishioners closed their eyes to pray during a June 2015 Bible study at the historically black Emanuel AME Church.
The official spoke on a condition of anonymity because he wasn't authorised to speak publicly about the case.
Roof will be taken to a federal prison in another state, where he will await his execution on charges of hate crimes and obstruction of the practice of religion.
More From This Section
The deal with state prosecutors, who also had been pursuing the death penalty, comes in exchange for a life prison sentence on the state charges.
Survivors of the shooting also spoke in court during the trial, evoking chilling images of the bloody Wednesday night tableau. Jennifer Pinckney, the widow of slain pastor and state Sen. Clementa Pinckney, brought some jurors to tears with her description of how she shielded her young daughter in her husband's office as the bullets rang out in the nearby fellowship hall.
"I have the right to ask you to give me a life sentence, but I'm not sure what good it would do anyway," Roof told jurors in his closing argument. "I still feel like I had to do it.