The protesters began chanting "black lives matter" a few minutes into her speech.
At first, the former secretary of state acknowledged them: "Yes they do and I'm gonna talk a lot about that in a minute," she said.
She then tried ignoring the protesters, shouting her remarks over the chants.
"I have some issues to discuss and proposals to make if our friends will allow me to do it. They may actually find them to their liking," Clinton said, while continuing to speak over the disruption, one of the loudest she had faced on the campaign trail.
As the protests continued, Clinton supporters began chanting "Let her talk, Let her talk." Others chanted, "Hillary! Hillary" very loudly, seemingly to drown out the protesters.
Rep. John Lewis, a civil rights icon who had introduced Clinton just minutes before, personally tried to break up the protests, putting his hands on the shoulders of the protesters and speaking with them.
That effectively quelled the protesters, who were escorted out shortly after the uproar.
Friday evening, #AUCShutItDown, an Atlanta-based group affiliated with Black Lives Matter, said in a statement that they protested Clinton's event so they could press her to directly address issues facing the African-American community, particularly in regard to policing.
"Unfortunately, rhetoric DOES NOT save us, nor does it give confidence to black voters that we can trust Hillary to prioritize the necessity of ensuring our safety," the group said. "We've been waiting for weeks to see the platform that addresses these issues from Hillary Clinton's campaign. We will wait no more."
Clinton went on finishing her speech -- which focused on criminal justice reform and race -- to sizable applause from the crowd.
"I am glad the congressman and the mayor have my back," she said, acknowledging that Lewis and Atlanta Mayor Kasim Reed had joined her on stage.
Nick Merrill, a spokesman for Clinton, said the candidate would not meet with the protesters.
After walking off stage, Clinton was met by LaDavia Drane, her director of African-American outreach.
"It's always an adventure," Clinton proclaimed.
Speaking to CNN after the event, Lewis said he believes the protesters "represent another time, another period."
"It is unfortunate that they didn't listen to the secretary," he added.