In 1999, Buh Buh Ray and D-Von Dudley joined the World Wrestling Federation, where the "Buh Buh" stutter-spelling of "Bubba Ray Dudley" was rescinded. 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 two critically acclaimed Tables, Ladders, and Chairs matches, the first at SummerSlam in 2000 and the second at WrestleMania X-Seven. While they were initially heels, one of the things Bubba Ray was known for was driving women through tables including WWE Divas Terri, Mae Young, Lita, Trish Stratus, Tori Torrie Wilson, Stacy Keibler and Jazz. The Dudley Boyz were soon cheered by the crowd and were turned face in early 2000. On the December 28, 2000 episode of SmackDown!, Bubba received a title shot against WWF Champion Kurt Angle, which he lost after an Angle Slam through a table. In early 2001, The Dudleys were joined in the WWF by Spike Dudley.
In mid-2001, the Dudley Boyz turned heel once again by joining The Alliance, a large stable of former ECW and other invading wrestlers led by Shane McMahon and Stephanie McMahon-Helmsley who attempted to take over the WWF (Spike, along with several other ECW alumni, did not join The Alliance). The Invasion ended at the Survivor Series, when five WWF wrestlers defeated five Alliance wrestlers in a match to determine the ownership of the WWF. The Alliance disbanded and its members left the WWF, but the Dudley Boyz retained their jobs due to their possession of the WWF Tag Team Championships.
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 Bubba Ray was drafted to Raw and D-Von to SmackDown!. On Raw, Bubba Ray found moderate success as he competed for the WWE Hardcore Championship, formed a tag team with Spike, and even competed in a World Heavyweight Championship match against Triple H. D-Von's new gimmick on SmackDown! failed to get over, however, and he was reunited with Bubba and Spike on November 17, 2002 when he returned to the Raw brand.
The Dudley Boyz became a staple 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 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. Shortly after arriving on SmackDown!, the Dudley Boyz turned heel once again, siding with Paul Heyman and feuding with Rob Van Dam and Rey Mysterio. On May 27, the Dudley Boyz kidnapped Paul Bearer, the manager of Heyman's enemy The Undertaker. On June 27 at The Great American Bash, The Undertaker defeated the Dudley Boyz in a handicap match. In July, the Dudley Boyz reunited with Spike. For the remainder of the year, they assisted Spike in his matches for the WWE Cruiserweight Championship. They also won the WWE Tag Team Championship one more time. In early 2005, the Dudley Boyz were removed from WWE television while the WWE creative team attempted to devise an angle 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 General Manager 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 of the night after driving Dreamer through a flaming table. On July 5, 2005, WWE announced that it had opted not to continue contract renewal negotiations with the Dudley Boyz.
On January 25, 2015 at Royal Rumble in Philadelphia, Bubba Ray returned to WWE and competed in the Royal Rumble match as a surprise entrant, at number 3. He and R-Truth performed the signature moves of the Dudley Boyz on The Miz, before Dudley eliminated both Miz and Truth. He was later eliminated by Bray Wyatt.
On the August 24, 2015, episode of Monday Night Raw, he and D-Von Dudley made a surprise return to the WWE, reviving their Dudley Boyz tag team persona. They attacked the WWE Tag Team Champions, the New Day, and gave a 3D through a table on Xavier Woods. They made their in-ring return the following Thursday on SmackDown, where they defeated The Ascension. On the August 31 Raw, they defeated The New Day in a tag match, therefore putting them in contention for the tag titles. On the September 3 episode of SmackDown The Dudley Boyz defeated The Prime Time Players. The Dudley Boyz would be granted their tag title opportunity on the September 14 Raw, against the New Day at Night of Champions. They were, however, unsuccessful in the bout. The Dudleys would get two more chances for the tag titles at WWE Live From Madison Square Garden and at Hell in a Cell, but both matches were won by the New Day.
In December, The Dudley Boyz began a rivalry with The Wyatt Family, and later aligned themselves with the returning Rhyno and Tommy Dreamer in the feud. At TLC: Tables, Ladders and Chairs, The Wyatt Family defeated Team ECW in an eight-man elimination tables match. At the 2016 Royal Rumble kickoff, The Dudleyz, The Ascension, Mark Henry & Jack Swagger and Damien Sandow & Darren Young competed in a Fatal 4-Way Tag Team Match to qualify for the Royal Rumble match itself, with Swagger and Henry getting the win.
On the February 8th Raw, Bubba Ray and D-Von attacked The Usos after a match involving them against The New Day and Mark Henry. On the following Smackdown, Bubba Ray cemented the team's heel turn by saying that The Dudley Boyz are the "baddest team on the planet", and returned to the WWE to add to their legacy. He further claimed that the fans think they are a nostalgia act, so they will no longer use tables; forcing officials to carry several of them to the backstage area. On the WrestleMania 32 pre-show, The Dudley Boyz lost to the The Usos. However after the match, The Usos would eventually put The Dudleyz Boyz through a table each. The following night on Raw, The Dudley Boyz won a rematch in a tables match. After the match, Enzo Amore and Colin Cassidy would come out and "trash talk" The Dudley Boyz. In a tournament set up by Shane McMahon to determine the new number 1 contenders to the WWE Tag Team Championship, they would defeat The Lucha Dragons to advance to the semi-finals, where they clashed with Enzo Amore and Colin Cassady in a losing effort. On July 19 at the 2016 WWE draft, the Dudley Boyz were drafted to Raw. At SummerSlam, they would lose to Sami Zayn and Neville.
The day after SummerSlam, the Dudley Boyz announced that they were announcing their departure from WWE on that night's Raw. During their farewell segment, they were confronted by The Shining Stars. After receiving insults from The Shining Stars, the Dudley Boyz attacked them, turning face once again in the process. As they set up Primo for a 3D through a table, Luke Gallows and Karl Anderson attacked both Bubba Ray and D-Von, sending D-Von through the table.