Jones was selected by the Atlanta Braves in the 1st round (1st pick) of the 1990 amateur draft. He made a quick jump through the minors to make his major league debut on September 11, 1993.

After sitting out the entire 1994 season with an ACL tear in his left knee, Jones came back strong in 1995, leading all major league rookies in RBI (86), games played (145), games started (123), plate appearances (602), at-bats (524), and runs scored (87). He eventually went on to win The Sporting News Rookie of the Year Award.

In 1999, Jones won the National League MVP award after hitting .319 with 45 home runs and 110 RBI. Jones led the Braves to the World Series against the New York Yankees that year. 

He is the only switch hitter in Major League Baseball history to have a .300+ career batting average and more than 300 home runs. He played his entire career with the Braves compiling a total of over 2,600 hits, 1600 runs, 500 doubles, 1600 RBI's and 460 home runs.