During his first two years with the Atlanta Braves, Jones most often appeared as a right fielder. However, since then, he has played exclusively in center field. Aside from , when he appeared in 32 games, Jones appeared in 150 or more games in each year of his career up to , when only appeared in 75 games.
He has appeared in the All-Star Game five times and he won both the Hank Aaron Award and a Silver Slugger Award for outfielders in . In , he was the inaugural National League All-Star Final Vote winner.
In Game 1 of the 1996 World Series on October 20, 1996, Jones was able to demonstrate his talents on the national stage. He connected for two home runs to left field on his first two at-bats as the Braves routed the New York Yankees 12-1. Jones became the youngest player ever to homer in the World Series (breaking Mickey Mantle's record - on Mantle's birthday.)
Whether he was in the batter's box or gliding under a fly ball to make a casual basket catch, Jones played the game in a very relaxed manner. This temporarily earned him the ire of manager Bobby Cox in June 1998 in an incident in which Cox pulled Jones out of a game because he felt Jones had lazily allowed a single to drop in center field.
Still only 22 years old, Jones had similar numbers in , and though he was a dependable (he played all 162 games that season) and good player, many began to wonder if or when he would live up to the potential that they believed he possessed. He had a mini-breakout season in with, up to that point, career highs in average (.303), homers (36), and RBI (104). He also earned his first All-Star appearance.
However, in his average fell and his strikeouts went up. By now, Jones had gained nearly 30 pounds since reaching the majors, greatly diminishing his speed on the basepaths (he would not steal more than 11 bases after 2001). He maintained similar numbers in 2002, but was still playing superb defense. In , with power-hitting Gary Sheffield in the lineup, Jones set a new career high in RBI (116). Unfortunately, he took a step backward in when he hit fewer than 30 homers and struck out 147 times.
Prior to the 2005 season, Jones increased his workout regimen and, following advice given by Hall of Famer Willie Mays, widened his batting stance. The result was his most productive offensive season ever. Jones hit a major league-leading 51 home runs, surpassing Hank Aaron's and Eddie Mathews' single-season club record. He also led the National League with a career-high 128 RBI. Jones' torrid hitting in the summer, especially while teammate Chipper Jones was out with an injury, helped carry the Braves to their 14th consecutive division championship. He finished just behind St. Louis Cardinals' first baseman Albert Pujols in the 2005 NL MVP vote.
Coming into the last year of his contract with the Braves, many fans and sports analysts alike felt that 2007 would be the last year in which Jones would be a Brave, mostly because of his potential value on the market that the Braves would not be able to afford. Jones, however, had an unexpectedly poor start to the season, striking out 51 times in 41 games and carrying a batting average in the low .200s for the majority of April and May.
On April 30, Jones hit a three-run walk-off home run against the Philadelphia Phillies. On May 28, Jones hit his 350th career homer off Chris Capuano. After the All-Star break, Jones continued to have productive power numbers; however, his batting average remained poor.
On October 2, the Braves announced they would not be bringing Jones back for the 2008 season.
On December 5, 2007, Jones agreed to a two-year deal with the Los Angeles Dodgers, worth $36.2 million. He continued to struggle, hitting below .200 for most of the season. Additionally, he had only 10 hits in 116 at-bats with runners in scoring position. Due to his lack of production, Jones was dropped to eighth in the Dodger line-up. This was the first time since 1998 that Jones had hit eighth in any line-up.
On July 27, 2008, Dodgers manager Joe Torre benched Jones and said he would only be used as a spot starter in the future, effectively giving up on the season. On the day he was benched Jones had a .166 batting average, two home runs and 12 RBI coupled with 68 strikeouts in 187 at-bats..
On September 13, 2008, Jones was put on the 60-day disabled list, effectively ending his disappointing season. Jones finished the season with a .158 batting average, three home runs, and 14 RBI.