In the summer of 1999, Buh Buh Ray and D-Von left ECW following a pay dispute and joined the World Wrestling Federation, debuting in September.. Throughout 2000 and 2001, the Dudley Boyz engaged in a three way feud for the WWF Tag Team Championship with the Hardy Boyz and Edge and Christian. The feud incorporated the first triangle ladder match at WrestleMania 2000, and two Tables, Ladders, and Chairs matches, the first at SummerSlam in August 2000 and the second at WrestleMania X-Seven. While they were initially villains and were known for driving women through tables, the Dudley Boyz became fan favorites in early 2000. In early 2001, they were joined in the WWF by Spike Dudley. In late 2001, the Dudley Boyz won the WWF Tag Team Championship, which they unified with the WCW Tag Team Championship during The Invasion, a storyline where the wrestlers from World Championship Wrestling and Extreme Championship Wrestling "invaded" the WWF.
Following WrestleMania X8, in May 2002 the WWF was renamed "World Wrestling Entertainment" (WWE) and the roster was divided into two brands, Raw and SmackDown!. The Dudley Boyz were separated when Hughes was drafted to SmackDown! and Bubba Ray ended up on Raw. Hughes became a villainous reverend character alongside his protégé Deacon Bautista. Though the gimmick was a launching platform for Batista's career, it didn't last long and Hughes was betrayed by Batista and he eventually was reunited with Bubba Ray and Spike on November 17, 2002 when he returned to Raw. The Dudley Boyz became a stable in the Raw tag team division over the next sixteen months, feuding with teams such as 3-Minute Warning, La Résistance, and various combinations of the The Un-Americans. They held the WWF World Tag Team Championship several more times before being traded (along with Booker T) to SmackDown! on March 22, 2004 in exchange for Triple H.
On May 27, 2004 the Dudley Boyz kidnapped Paul Bearer, the manager of Paul Heyman's enemy The Undertaker. On June 27, 2004 at The Great American Bash, The Undertaker defeated the Dudley Boyz in a handicap match. They also won the WWE Tag Team Championships one more time but were upset by the high-flying team of Paul London and Billy Kidman. In July 2004, the Dudley Boyz reunited with Spike. For the remainder of the year, they assisted Spike in his matches for the WWE Cruiserweight Championship. In early 2005, the Dudley Boyz were removed from WWE television and sent to Ohio Valley Wrestling while the WWE creative team attempted to devise a storyline for them. The Dudley Boyz returned to WWE television in June 2005 in order to promote ECW One Night Stand, an ECW reunion show.In the weeks preceding One Night Stand they, along with several other ECW alumni, vied with former WCW President Eric Bischoff and his "anti-hardcore crusaders". At One Night Stand on June 12, the Dudley Boyz defeated Tommy Dreamer and The Sandman in the main event.
On July 5, 2005, WWE announced that it had opted not to continue contract renewal negotiations with the Dudley Boyz. In August 2005, they were issued with legal notices instructing them not to use the (WWE trademarked) name "Dudley". Soon after, LoMonaco and Hughes (D-Von) announced that they intended to pursue legal action against WWE.