While Carlito was recovering from an injury, he was involved in a comical angle with SmackDown!'s general manager, Theodore Long. The storyline consisted of Carlito being forced to do demeaning chores around the arena, such as selling hot dogs, removing snow from parking lots with a shovel and mopping floors. As a result of these actions, Carlito created a petition in support of Long’s destitution, but was unsuccessful. On March 26, 2005, Colón performed for the first time in six months as Carlito, in a match against his younger brother Eddie Colón during an event in Caguas, Puerto Rico. Carlito made his WrestleMania debut in a non-wrestling role at WrestleMania 21, in which he interrupted an edition of Rowdy Roddy Piper's Piper's Pit, with Stone Cold Steve Austin as the special guest. This event led to an angle in the World Wrestling Council, where Piper and Carlito were booked to wrestle a match on Friday Madness, a special event presented by the company, which Piper won. Following WrestleMania, Carlito created an interview segment entitled Carlito’s Cabana. Carlito then entered a feud with The Big Show after a spot where Show refused an offer to work in an enforcer role for Carlito. This feud involved Carlito tricking Show into eating a poisoned apple, and Matt Morgan becoming Carlito's enforcer. This feud ended with Carlito defeating Show at Judgment Day.
Carlito was drafted to the Raw brand in the 2005 WWE Draft Lottery, where he defeated Shelton Benjamin for the WWE Intercontinental Championship in his debut match. He then lost the Intercontinental title to Ric Flair at Unforgiven. Towards the end of 2005, Carlito was involved in a brand rivalry which led to him discontinuing Carlito’s Cabana. The angle concluded with Carlito wrestling for Team Raw against Team SmackDown! in a ten man tag team match at the Survivor Series.
In late 2005, Carlito was added to angles involving the WWE Championship. After defeating Shelton Benjamin in a qualifying match, Carlito was added to the main event at New Year's Revolution in early 2006, the Elimination Chamber match. He was one of the final two wrestlers remaining, after eliminating Kane, Chris Masters and Shawn Michaels. He then lost the match to John Cena.
Carlito appeared in another World Wrestling Council show that took place on March 15, 2006 in Carolina, Puerto Rico. He defeated Tyson Tomko, and he hosted an edition of Carlito's Cabana with Victor Jovica and Carlos Colón. Following this segment, Carlito did a sudden face turn when he attacked a heel stable led by Rico Suave.
Following New Year’s Revolution, Carlito and Chris Masters joined forces as a tag team. Together they competed against Kane and Big Show for the World Tag Team Championship at WrestleMania 22. Carlito and Masters lost when Masters accidentally attacked Carlito. Following the match, Carlito confronted Masters, igniting a feud between them. This storyline came to a conclusion at Backlash, where Carlito defeated Masters via an illegal assist from the ropes.
At Vengeance, Carlito fought in a Triple Threat match against Shelton Benjamin and Johnny Nitro for Benjamin's Intercontinental title. Nitro won the match after pulling Carlito outside of the ring and pinning him. Following Vengeance, Carlito began an on-screen relationship with Trish Stratus. He also engaged in a short feud with Johnny Nitro and Melina, which ended after Carlito and Stratus defeated Nitro and Melina in a mixed tag team match at Saturday Night's Main Event. Carlito next feuded with Randy Orton, following a spot where Orton attempted to attack Stratus during a backstage segment. The two wrestlers were booked for a match at Unforgiven and a rematch on Raw; Orton won both matches. The feud concluded in a match at WWE’s annual Tribute to the Troops event, where Carlito won by pinfall. The angle involving Carlito's relationship with Trish Stratus lasted until Stratus' retirement from wrestling following Unforgiven.
In the final months of 2006, Carlito competed in several matches involving the Intercontinental Championship. His involvement in this angle ended at Cyber Sunday 2006, after being elected by the fans to face Jeff Hardy for the championship. Carlito, however, lost the match. During this time period Carlito's gimmick underwent a slight change and was sold as a "ladies man", eventually getting involved in another fictional relationship with Torrie Wilson. Carlito participated in the 2007 Royal Rumble, where he was eliminated by The Great Khali. Following the Royal Rumble, Carlito started a feud with Ric Flair, in which Flair insulted Carlito for leaving a show early by claiming that he had no heart, no passion and was undeserving of his spot on the roster. After Carlito challenged and lost to Flair in a match, they were booked as a tag team, with Flair serving as a mentor to Carlito. The team was involved in a Money in the Bank qualifying match which was declared a "no contest" after The Great Khali interfered. This led to a triple threat match the following week which included and was won by Randy Orton.
Prior to the WrestleMania 23, Colón expressed dissatisfaction with WWE management in an interview for not having plans to book him to appear at the pay-per-view and criticized their methods for selecting performers to push, making reference to backstage politics. Carlito, however, did participate in a dark match at WrestleMania, winning in a tag team match with Flair as his partner against the team of Chavo Guerrero and Gregory Helms. The team also lost a number one contender's match for the World Tag Team Championship against Lance Cade and Trevor Murdoch. Carlito turned on Flair after the loss. Their feud ended with a match at Judgment Day, where Carlito lost to Flair by submission.
Following his feud with Flair he was involved in angles with The Sandman and Triple H. He then lost to Triple H at Unforgiven 2007 in a no disqualification match where the no disqualification rule only applied to Carlito. In late 2007, Colón requested his release from the WWE as he was unhappy with the direction of his character. Following a meeting with Vince McMahon, however, he was convinced to stay. On December 10, 2007, he was featured in a ladder match at the Raw 15th Anniversary against Jeff Hardy for the WWE Intercontinental Championship, which Hardy won.
Carlito then formed a tag team with Santino Marella. The team was placed in several matches involving the World Tag Team Championship, twice being named the number one contenders; however, they lost the relevant championship matches.
As part of the 2008 WWE Supplemental Draft, Carlito was drafted back to the SmackDown brand.
On September 12, he re-debuted on the brand as a face, forming a tag team with his brother, Primo. They defeated WWE Tag Team Champions Curt Hawkins and Zack Ryder in the match to gain their first victory as a team. Two weeks later, both teams competed in a title match, with The Colóns winning to become tag team champions. Subsequently, Carlito and Primo entered a feud with World Tag Team Champions John Morrison and The Miz. At WrestleMania XXV, The Colóns defeated Miz and Morrison in a tag team unification match, becoming the first team to simultaneously hold both sets of the company's Tag Team Championships since their creation.
On April 15, 2009, both Carlito and Primo were drafted back to the Raw brand as part of the 2009 Supplemental Draft. At The Bash, the duo dropped the Unified Tag Team Titles to Edge and Chris Jericho in a Triple Threat Tag Team Match also involving Ted DiBiase and Cody Rhodes. Carlito and Primo invoked their rematch clause the next night on Raw, but were unsuccessful. On the July 6 episode of Raw, they lost to Edge and Jericho, and afterwards Carlito attacked Primo thus ending the Colons' partnership and turning Carlito into a heel once again in the process. The feud between Primo and Carlito ended after Carlito beat Primo in a match after a Back Stabber. Carlito then faced Kofi Kingston for the United States Championship but lost and once again lost in a Fatal Four Way Match against Kofi Kingston, The Miz and Jack Swagger. For a little while, Carlito was managed by Rosa Mendes but the two have since been split up with Rosa being drafted to ECW as a part of a tri-branded diva trade. He returned to Raw after days of inactivity, by telling John Cena that he doesn't deserve the WWE Champion Belt. Carlito then bit into an apple, and was about to spit in his face, when John Cena did the Attitude Adjustment. The next week on Raw, he was defeated by John Cena. At the 2009 Slammy Awards he, Chris Masters, and Eve Torres hosted The Extreme Moment Of The Year. Jeff Hardy won the award, but Matt Hardy took it. In the middle of Matt's speech, Carlito asked him why he was accepting the award? Then Carlito punched him and Chris Masters put him in a Masterlock, taking him breathless. The next week, he faced Chris Masters, and fainted from the Masterlock again.