In 1989, Yates was hired as Assistant U.S. Attorney by Bob Barr for the U.S. Attorney's Office for the Northern District of Georgia. Early in her career at the Department of Justice, Yates prosecuted a variety of types of cases including white-collar fraud and political corruption. In 1994, she became Chief of the Fraud and Public Corruption Section. She was the lead prosecutor in the case of Eric Rudolph, who committed the Centennial Olympic Park bombing, a terrorist convicted for a series of anti-abortion and anti-gay bombings across the southern United States between 1996 and 1998, which killed two people and injured over 120 others. She rose to First Assistant U.S. Attorney in 2002 and to Acting U.S. Attorney in 2004. In the U.S. Attorney's office she held leadership positions under both Republican and Democratic administrations.