After WCW was purchased by the World Wrestling Federation (WWF) in March 2001, Moore signed a contract with them and was assigned to the Heartland Wrestling Association (HWA), a Louisville-based WWF developmental territory. He teamed with Karagias in HWA until Karagias was released by the WWF. Moore would make his TV debut on the July 13, 2002 episode of Velocity.
In 2003, after competing in the cruiserweight division for several months as a fan favorite, Moore became a villainous acolyte of Matt Hardy, who had begun proselytizing a philosophy known as "Mattitude" and calling himself "Matt Hardy Version 1.0". Moore became a "Mattitude Follower" (abbreviated "MF'er") and started dressing like Hardy and accompanying him to ringside. Moore often lost to more physically dominant opponents or unsuccessfully attempted to help Hardy win his matches, both things that resulted in Hardy attacking Moore in order to vent his frustrations, claiming that he had "failed to comprehend [Hardy's] coaching!" Moore did, however, assist Hardy in his bid to lose several pounds in order to qualify for a WWE Cruiserweight Championship title shot, which he won when Moore came through again, this time distracting then face, Billy Kidman to enable Hardy to get the win and the title. On April 24, Crash Holly also became an MF'er. He was subordinate to Moore and, as such, was referred to as a "Moore-on". The group was short-lived, though, as Crash was released from WWE on June 30.
Moore and Hardy continued to work together until November 17, when Hardy left SmackDown! and joined the Raw brand. As a result, Moore was a fan favorite again and Paul Heyman (SmackDown!'s then-general manager) decided to punish Hardy vicariously for leaving his show by forcing Moore to face a series of much larger opponents. In successive weeks, Moore was squashed by Matt Morgan, Nathan Jones, and The Big Show, before unexpectedly defeating A-Train in an upset victory on the December 11 episode of SmackDown!. The following week, WWE Champion Brock Lesnar was scheduled to defend his title against a random wrestler, with the name of his opponent selected arbitrarily by a lottery machine. Moore was selected as Lesnar's opponent, and Lesnar defeated him with ease and then revealed that all the balls had borne Moore's name, with Lesnar having rigged the process in order to ensure that he would have a much smaller opponent. Immediately after the match, Moore and Hardcore Holly were scheduled to face A-Train and Morgan in a tag team match, with Holly gaining a title shot if he won and being fired if he lost. Despite Moore being incapacitated, he and Holly were able to win the match.
In 2004, at WrestleMania XX Moore took part in a "Cruiserweight Open" for the Cruiserweight Championship, but was eliminated by Último Dragón. His next high profile appearance was on the July 8, 2004 episode of SmackDown!, which saw Moore wrestle under a mask as "El Gran Luchadore". Moore faced John "Bradshaw" Layfield (JBL) in the match for the WWE Championship and was initially dominated by his much larger opponent. A second Luchadore (the disguised Eddie Guerrero), however, took Moore's place, prompting Layfield to run away, thus giving Moore the victory by count out.
Moore competed in the cruiserweight division and as a jobber for the remainder of 2004 and the first half of 2005. In early 2005 he adopted the gimmick of a punk and began wearing punk clothing to the ring. On March 21, 2005 he was concussed and suffered whiplash after his Hummer was involved in a head-on collision with a vehicle driven by an inebriated United States Army Sergeant in Fort Bragg, North Carolina. He quickly recovered from his injuries, but was released by WWE on July 5, 2005.
On March 14, 2006, wrestling journalist Dave Meltzer claimed that Moore had committed to a verbal agreement with World Wrestling Entertainment (WWE). Three days later, WWE.com confirmed and released an interview with Moore talking about his imminent return to the company.In July 2006, Moore became a villain again and was part of WWE's ECW brand, making his first appearances in vignettes and calling himself "The Reject," while still dressed in the fashion of his "Prince of Punk" gimmick. His in ring debut was a loss to CM Punk on September 12, a week after Punk had confronted Moore and called him a "poser" before slapping him across the face. After one more loss to Punk, Moore was a face once more and relegated to jobber status on the ECW brand, making only sporadic appearances.
On the February 16, 2007 edition of SmackDown! Moore suddenly switched brands, appearing in an in-ring brawl with other SmackDown! cruiserweights, which was itself a prelude to a "Cruiserweight Open" at No Way Out, which Moore also took part in, but was eliminated by the defending Cruiserweight Champion Gregory Helms. Moore then established himself as a fan favorite after teaming up with Scotty 2 Hotty and Jimmy Wang Yang in a six-man tag team match against several villainous cruiserweights. Moore returned to television on the June 15 edition of SmackDown!, no longer in his "Prince of Punk" attire, competing in a Fatal Four Way number one contender match for the Cruiserweight Championship, which was won by Wang Yang and also involved Daivari and Jamie Noble. On the June 22 edition of SmackDown!, Moore teamed with Wang Yang in a losing effort against Chavo Guerrero and Noble.
Moore now had a new look with long hair similar to his first look. He was also seen competing in the 20-man battle royal for the World Heavyweight Championship and was the third person to be eliminated. He also competed in the "Cruiserweight Open" at The Great American Bash along with Noble, Funaki, Wang Yang, and Guerrero. The match was inadvertently won by Hornswoggle. Moore then faced Noble and Guerrero, respectively, in losing efforts. Shannon was also used in backstage skits with Noble, Finlay and Kane. Shannon also teamed with Eugene against Deuce 'n Domino in losing efforts. On the September 14 episode of SmackDown!, however, he defeated Noble in a singles match. This was the first time Moore had won a singles match in WWE since 2005.
On December 18 Moore and Wang Yang defeated the WWE Tag Team Champions John Morrison and The Miz to earn a title-shot, igniting a feud between the two teams. On January 1, 2008, Moore and Wang Yang once again beat Morrison and the Miz, this time in a six-person tag team match also involving Layla and Kelly Kelly. The following week, in a Fifteen Minutes of Fame Match, Moore and Wang Yang tied the champions on pinfalls, meaning Miz and Morrison retained the titles. Moore and Yang feuded on and off with Miz and Morrison for the next few months, winning singles matches against them during April. Moore and Yang received another WWE Tag Team Championship match, on the May 2 edition of SmackDown, but failed to win the titles.
After this feud ended, he was rarely utilised, and on August 8, 2008, WWE announced that Moore had been released from his WWE contract.