In 1992 Miller was critically important to Arkansas governor Bill Clinton's campaign to secure the Democratic U.S. presidential nomination. Miller and Clinton seemed to be natural allies—both were active, moderate governors of southern states who had won office by promising to improve education. Further, they shared political advisors. Clinton's 1992 campaign strategists had worked for Miller in 1990. After Clinton won the presidential primary in Georgia, he invited Miller to give one of the three keynote speeches at the Democratic National Convention. Placards reading "Give'm Hell, Zell" were distributed among the delegates as Miller gave a speech that was critical of U.S. president George H. W. Bush's administration. Later that year, Miller again actively campaigned for Clinton, who carried Georgia in his win of the November presidential election. After such successes in state and national politics, it surprised few when Miller announced that he would seek a second gubernatorial term.
Miller's reelection campaign in 1994 was not easy. In spite of his successes, Miller had made political enemies. Miller had tried, unsuccessfully, to have the Confederate battle emblem removed from the state flag. The governor's close connection to President Clinton was also detrimental to Miller as the president's popularity sagged. Finally, the fact that Miller had retreated on his pledge to serve only one term as governor irked some voters. Miller's Republican opponent in 1994 was Guy Millner, a millionaire who was willing to spend his own fortune to finance his campaign. Miller ultimately prevailed but only by a narrow margin—Miller received 51.05 percent of the votes, and Millner received 48.95 percent, a margin of just 32,555 votes.
During his second term as governor, Miller continued his efforts to improve all levels of education in Georgia by making investments in technology, buildings, and human resources. Georgia became known as a national leader for innovative programs, and teachers' salaries rose to near the top for the region. In the last year of his governorship, Miller secured private funding to distribute classical music CDs to the family of every baby born in the state. (At the time, research indicated that playing classical music to newborns may increase their intelligence.) Miller also ordered state agencies to make budget cuts and redistributions—unusual for a state in good financial shape. His reasoning was that state agencies likely had become wasteful in their spending during the prosperous 1990s. Miller left office in early 1999 with an 85 percent approval rating from Georgians—a record high for a Georgia governor and a rating that made him the most popular governor in the nation.