Prior to Franklin's term, Atlanta's combined sewer system violated the federal Clean Water Act and burdened the city government with fines from the Environmental Protection Agency.

In 2002, Franklin announced an initiative called "Clean Water Atlanta" to address the problem and begin improving the city's sewer system.

[8] With solid popular support and strong backing from the business sector, Franklin was reelected Atlanta Mayor in 2005, garnering more than 90 percent of the vote.

[10] In February 2006, The White House Project named Shirley Franklin one of its "8 in '08", a group of eight female politicians who could possibly run and/or be elected president in 2008.

In 2008, facing a major deficit, Mayor Franklin asked the Atlanta City Council to approve a property tax increase, to avoid public safety cuts.

As Mayor Franklin warned, without the tax increase, layoffs and pay cuts of Atlanta public safety officials would be imminent.

In fact, according to the Atlanta Business Chronicle city spending actually ran slightly below budgeted amounts through the first quarter of the fiscal year that began in July.

Franklin, along with Philadelphia's Michael Nutter and Phil Gordon of Phoenix, lobbied Treasury Secretary Henry Paulson in a joint letter asking for a share of the proposed $700 billion bailout.

The foundation praised her management of the city of Atlanta during the critical period of enormous deficit and loss of public confidence in government following the corrupt administration of Mayor Bill Campbell.