Garrett Rolfe, who has already been fired, faces 11 charges related to Rayshard Brooks' death. If convicted, he could face the death penalty.
The other officer who was at the scene, Devin Brosnan, plans to testify as a witness in the case, officials said.
The case comes amid US protests over police killings of black Americans.
Lawmakers in Washington are currently debating new police reform laws.
Officer Brosnan - who has already been placed on administrative leave - will be charged with assault for standing on Mr Brooks' shoulder as he lay dying.
Officials said this was the ninth time that an Atlanta police officer had been prosecuted for homicide.
They added that it is believed to be the first time a police officer would testify against a member of his own unit.