They continued their storyline feud with Benoit until No Way Out, when Benoit teamed with Brock Lesnar to defeat Team Angle. The duo were scripted to win their first WWE Tag Team Championship just a month after their debut by defeating the champions, Los Guerreros (Eddie and Chavo Guerrero) on February 6, 2003. The two then went on to compete in their first WrestleMania match at WrestleMania XIX, retaining their tag title in a Triple Threat match against Los Guerreros, and Chris Benoit and Rhyno. Team Angle later lost the title to Eddie Guerrero and his new partner Tajiri at Judgment Day in a ladder match. The storyline concluded on the June 12, 2003 episode of SmackDown!, when Angle confronted Benjamin and Haas and fired them from Team Angle. They began referring to themselves as The World's Greatest Tag Team and won the tag title back on the July 3 episode of Smackdown. They lost the title on September 18, after Benjamin suffered a legitimate knee injury during a match against Los Guerreros. Benjamin was sidelined for approximately one month, but the pair competed together again, taking part in a Fatal Four-Way match at WrestleMania XX.
On March 22, 2004, Benjamin was drafted to the WWE Raw brand as part of the 2004 WWE Draft. After arriving, Benjamin quickly became a face when he scored an upset pinfall victory over Triple H. Benjamin then feuded with Triple H, beating him three times in total all: once by pinfall, once by count-out, and once by disqualification. As part of the storyline, Benjamin then feuded with the other members of Triple H's stable Evolution. Benjamin defeated Ric Flair at Backlash and lost to Randy Orton in an Intercontinental Championship match at Bad Blood.
During a match with Garrison Cade on WWE Heat, Benjamin punched Cade's knee brace, legitimately breaking his hand in the process and briefly taking him out of action. Benjamin returned in the fall of 2004 and was chosen by the fans to compete for the Intercontinental Championship in a match against then-champion Chris Jericho at Taboo Tuesday. Benjamin was scripted to win the match, giving him his first singles title in the company. During his reign as Intercontinental Champion, Benjamin retained the title against challengers such as Christian at Survivor Series, Maven at New Year's Revolution, and Chris Jericho at Backlash. Benjamin lost the title to Carlito when he debuted on Raw during the June 20, 2005 episode, ending the longest Intercontinental Championship reign of the decade.
Benjamin's next storyline began on the December 5, 2005 episode of Raw, when Shawn Michaels was scripted to give Benjamin a speech to get him "psyched" for their tag match together later in the night. As a part of the scripted ending to the match, Michaels was preparing to finish the match when Benjamin tagged himself in and missed a crossbody, allowing Carlito to pin Benjamin. Benjamin was then depicted as having a "losing streak" over the next several weeks, which led to Benjamin's noisy, scolding, and domineering Momma coming to Raw to confront Benjamin. Momma slapped and yelled at Benjamin every time he lost a match. Before long, she assisted Benjamin in his matches, often interfering on his behalf. This led to Benjamin once again becoming a villain. In 2006, Benjamin had a staged on-screen rivalry with then-Intercontinental Champion Ric Flair. On the February 20 episode of Raw, Benjamin defeated Flair to regain the Intercontinental Championship after Momma faked a heart problem, causing enough of a distraction to allow Benjamin to cheat and win the title. Benjamin continued to feud with Flair, but Momma no longer accompanied him to ringside. As part of the scripted events, Benjamin stated that she was undergoing heart surgery in the hospital and that he held Flair responsible.
Benjamin competed in the second Money in the Bank ladder match at WrestleMania 22. Benjamin then had an on-screen rivalry with the winner of that match, Rob Van Dam, in an attempt to take Van Dam's Money in the Bank contract. During this time, Benjamin emphasized his new heel persona with a new gimmick: wearing shades, jewelry, and occasional colored shirts while entering the ring. At one point, Benjamin was defeated by his former tag team partner, the returning Charlie Haas, during an episode of Raw. A predetermined stipulation added to this loss meant that Benjamin had to defend the Intercontinental Title in the same match as his shot at Van Dam's contract, meaning at Backlash it would be a "Winner Takes All" match. Rob Van Dam won at Backlash and became Intercontinental Champion. Benjamin regained the title from Rob Van Dam in a Tornado Tag Team match, pitting Benjamin, Triple H and Chris Masters against Van Dam and WWE Champion John Cena; both the WWE Championship and WWE Intercontinental Championship could be won by whoever pinned the appropriate champion. After Triple H Pedigreed Van Dam, he turned his attention to John Cena and went for the pin on the WWE Champion. Benjamin got to Van Dam first, picking up the pin and his third Intercontinental Championship. Subsequently, Benjamin feuded with Carlito and others for his Intercontinental Championship before losing the title to Johnny Nitro in a Triple Threat match also involving Carlito at Vengeance.
During December 2006, Benjamin's former tag team partner Charlie Haas came out to celebrate with Benjamin after he defeated Super Crazy. The World's Greatest Tag Team was officially reunited when they defeated The Highlanders on the December 11, 2006 episode of Raw. The duo feuded with Cryme Tyme and competed mainly on Heat.
On the November 20, 2007 airing of ECW on Sci Fi, Elijah Burke introduced Benjamin as the newest ECW superstar. Benjamin, who had dyed his hair blond before leaving Raw, began wearing gold wrestling attire and referring to himself as "The Gold Standard". On ECW, Benjamin began once again receiving more airtime and higher profile matches, defeating Tommy Dreamer in his debut. Benjamin then qualified for the Royal Rumble match and won an over the top rope preview. Benjamin appeared in the Rumble match, entering at number 17, but was eliminated by Shawn Michaels. He suffered his first loss since coming to ECW to Kane by count-out, on the January 29, 2008 episode of ECW on Sci Fi. On the February 22 episode of SmackDown!, Benjamin defeated Jimmy Wang Yang in a qualifying match for the Money in the Bank ladder match at WrestleMania XXIV, which was won by CM Punk. After WrestleMania, Benjamin briefly feuded with Punk, before he began an on-screen rivalry with Kofi Kingston, who defeated Benjamin on the April 22 episode of ECW. On ECW's 100th episode, however, Benjamin defeated Kingston, thus ending the latter's undefeated streak. To end the feud, Kingston then defeated Benjamin in an ECW Extreme Rules match.
As part of the 2008 Supplemental Draft, Benjamin was drafted to the SmackDown! brand. On the July 11, 2008 airing of SmackDown!, Benjamin defeated United States Champion Matt Hardy in a non-title match, earning himself a future title shot. At The Great American Bash, Benjamin once again defeated Hardy to win the United States Championship. Throughout his reign as champion, he retained the title several times against competitors such as R-Truth and Hurricane Helms. On the 500th episode of SmackDown!, on March 20, 2009 Benjamin lost his United States Championship to Montel Vontavious Porter, ending Benjamin's reign at 243 days. Benjamin then participated in the Money in the Bank ladder match at WrestleMania XXV, but failed to win as CM Punk won the match for the second year in a row. On June 29, 2009, Benjamin was traded back to the ECW brand. The following night, Benjamin returned to the brand in a losing effort to the debuting Yoshi Tatsu. However, he would defeat Tatsu in a rematch the following week on ECW. After a tag team match, Benjamin was attacked by his partner Sheamus after Benjamin was pinned. Over the following weeks, Benjamin and Sheamus began feuding with and traded wins against each other on ECW and Superstars, resulting in Benjamin becoming a face character. The feud lasted until Sheamus was moved to the Raw brand on October 26. The next night on ECW, Benjamin lost to Sheamus in Sheamus' final match on the brand. Benjamin wrestled Christian at TLC: Tables, Ladders & Chairs for the ECW Championship in a Ladder Match, but came up on the losing end. On the final episode of ECW on Syfy, Benjamin formed an alliance with Vladimir Kozlov. Together, they defeated three members of the ECW roster: Vance Archer, Caylen Croft and Trent Barreta. On the February 26th episode of Smackdown, Shelton Benjamin debuted, once again qualifying for the Money in The Bank Ladder Match at WrestleMania 26, beating CM Punk. However Benjamin failed to win the Ladder match. He defeated the returning Joey Mercury in his last match at the SmackDown tapings on April 20 in a dark match. On April 22, 2010, Benjamin was released from his WWE contract, along with Jimmy Wang Yang, Kung Fu Naki, Slam Master J, Mickie James and Katie Lea Burchill.
On March 8, 2011, Benjamin wrestled in a dark match prior to the SmackDown tapings in Houston, Texas, defeating Curt Hawkins.
On the July 26, 2016 episode of SmackDown, a vignette aired promoting Benjamin's WWE return.