Ms Bottoms, the city's second Black woman executive, confirmed that she would not run again on Friday, according to the Associated Press.
"Leadership sometimes is about passing off the baton," Ms Bottoms told reporters the day after issuing a press release announcing she would not run again.
The announcement was unexpected, particularly because Ms Bottoms was one of the individuals considered for Joe Biden's 2020 running mate.
Ms Bottoms said the decision was rooted in her faith, and denied that she was shying away from running a tough re-election campaign.
She pointed out that she had plenty of money to run with and the support of the president, but said regardless of her position she believes it’s her time to step away from the leadership position.
"There is a divine voice that lives inside each of us ... that may not make sense to anyone else.... But when you know what you know, it becomes less and less important what other people think," Ms Bottoms said.
She claimed that she had considered not running again since the start of her administration.
Ms Bottoms said she was not ruling out potentially taking a role in Joe Biden's administration in the future, but noted she felt more comfortable leaving knowing he was in the Oval Office.
"We'll see. I can tell you being mayor with President Biden in the White House has made a world of difference," she said.
White House press secretary Jen Psaki did not indicate that a post was available or would be in the short term for Ms Bottoms, but said she "remains of course someone who the president has a fondness for."
Ms Bottoms told donors that anyone who contributed to her reelection war chest would receive letters offering a refund for their donations.
She said she had no intentions of naming who she would prefer to take her spot, but she did say she would "make it known at the appropriate time who I will cast my vote for."
Felicia Moore, the president of the Atlanta City Council, has already announced she would run for the position.