In 1999, Bubba Ray and D-Von joined the WWF. Upon joining the company, Bubba Ray began to stutter during his promos. D-Von would then slap Bubba in the back of the head to help him get his words out. After several weeks, most of the gimmick was dropped.
While part of the WWF, the Dudley Boyz's claim to fame was bringing the use of tables as weapons into the wrestling mainstream, often using their signature double-team move, the 3D, to put their opponents through one of these tables. They were initially villains and were known for Bubba Ray's penchant for driving women (including Terri, Trish Stratus, Tori, B.B., Lita, Torrie Wilson, Jazz, Stacy Keibler, Molly Holly and Mae Young) through tables however they became fan favorites in mid-2000 when they engaged in a feud with T & A. They would then feud with D-Generation X which culminated in a tag team table dumpster match at King of the Ring 2000 in which Bubba drove Tori through a table. 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 Tables, Ladders and Chairs (TLC) matches, the first at SummerSlam in 2000. The second was at WrestleMania X-Seven in April 2001, in which Spike Dudley (who had joined the WWF in early-2001) interfered to aid the Dudleys.
In mid-2001, the Dudley Boyz became villains again by joining The Alliance, a massive group of wrestlers mostly consisting of invading ECW and other superstars led by Shane McMahon and Stephanie McMahon-Helmsley, who attempted to take over the WWF. During this time, the Dudleys acted as enforcers of the Alliance, interfering on the behalf of Alliance mid-carders and main eventers. Stacy Keibler became the Dudleys' manager during this time— dubbed the "Duchess of Dudleyville" by ECW manager Paul Heyman—but she later cost the Dudleys a tag team match, and they put her through a table. In 2002, their "little brother" Spike Dudley began to feud with them, winning the WWF Tag Team Title from them with partner Tazz.
Following WrestleMania X8 in March 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 for a short time when Bubba Ray was drafted to Raw and D-Von to SmackDown!. Bubba became a fan favorite again by reuniting with Spike Dudley while D-Von, who was still a villain, went on to become the corrupt preacher character "Reverend D-Von" and gained a protege with Deacon Batista. At Judgment Day in 2002, Bubba Ray was in the corner of Raw's Trish Stratus, who was defending the WWE Women's Championship against Keibler; D-Von and Batista were in Stacy's corner as asked by Mr. McMahon. After Stratus retained her title, Bubba Ray and D-Von stood in the ring and shook hands before an altercation broke out between the three men where D-Von and Batista ended up driving Bubba through a table. As 2002 went along, Bubba Ray teamed with Spike on Raw to form a new version of the Dudley Boyz.
Bubba and D-Von reunited following the Survivor Series, when D-Von helped Bubba Ray in a match. From then on, he was back on Raw (as he was part of a package deal that would send The Big Show to SmackDown!). After the Dudley Boyz were back together they immersed themselves in the Raw tag team division over the next sixteen months. During this time, alternating between siding with and feuding with Raw General Manager, Eric Bischoff. They continued competing in the tag team division until all three Dudleys were drafted/traded over to SmackDown! in March 2004, Bubba Ray and D-Von aligned with Paul Heyman and feuded with The Undertaker. They were also billed from New York City instead of Dudleyville. In June of that year, they won the SmackDown brand's WWE Tag Team Championship, making them the first team to hold both sets of tag team titles in WWE history. By July, the Dudleys were helping Spike win matches by interfering in his favor, which Spike seemed to dislike at first, only to reveal his hand as the "boss" of the outfit after they helped him take the WWE Cruiserweight Championship from Rey Mysterio.
After a lengthy hiatus, Bubba, D-Von, and Spike made what would be their final appearance at a WWE sanctioned event, when they were a part of the original One Night Stand in June 2005. In July 2005, WWE opted not to continue contract renewal negotiations with the Dudley Boyz. In addition, there was a mass of wrestlers (including Spike) that were released by WWE for budgetary reasons.
Bubba Ray made his return at the 2015 Royal Rumble as the third entry, but was eliminated by Bray Wyatt.
On the August 24, 2015 episode of Raw, the Dudley Boyz (both Bubba Ray and D-Von) officially returned to WWE as a face team when they attacked the New Day and gave a Dudley Death Drop to Xavier Woods through a table. The next night, at the tapings for the August 27 Smackdown, they wrestled their first match back, defeating The Ascension. After the match they would go on to put Viktor through a table. At Night of Champions and WWE Live from Madison Square Garden, the Dudley Boyz faced The New Day for the titles and won by disqualification, but these victories allowed The New Day to retain the titles. At Hell in a Cell, the Dudley Boyz, once again, were unsuccessful in their challenge. At Survivor Series, the Dudley Boyz would team with Titus O'Neil, Neville and Goldust to defeat Stardust, The Ascension, Bo Dallas and The Miz in a 5-on-5 traditional Survivor Series elimination tag team match. The following night on Raw, the Dudleys suffered a defeat against Bray Wyatt and Luke Harper of The Wyatt Family. The following night on Smackdown!, the Dudley Boyz faced the Wyatt Family again, beating Erick Rowan and Braun Strowman by disqualification after Luke Harper attacked Bubba Ray and threw him through his own table. The next Raw, they had a no-contest six man tag team match against Rowan, Harper and Strowman when the Dudleys teamed with the returning Tommy Dreamer. However, the Dudleys and Dreamer fended off a post-match assault and threw Wyatt into a table. At TLC: Tables, Ladders and Chairs (2015), Team Extreme (The Dudleys, Dreamer, and Rhyno) were defeated by The Wyatt Family (Bray Wyatt, Luke Harper, Erick Rowan and Braun Strowman) in a elimination tables match. The next night on Monday Night Raw, the Dudley Boyz, Tommy Dreamer, and Rhyno, were defeated again by The Wyatt Family in an 8-man tag team Extreme Rules Match.
On the February 8 episode of Raw, the Dudley Boyz turned heel for the first time since their return to WWE when they attacked The Usos after an 8-man tag team tables match that also featured The New Day and Mark Henry. Only three days later on SmackDown, the Dudley Boyz proclaimed that their signature tables didn't win all those Tag Team Championships for them, but rather they did it themselves, and thus, with the help of several stage-hands and staff members, they took all the tables they had out of the arena, going "table-free" for the first time in their careers. On March 14, 2016 it was announced via the WWE App immediately after Raw went off the air that the Dudley Boyz would face The Usos in their first WrestleMania since WrestleMania XX. However the match was soon moved to the Wrestlemania 32 kickoff show instead, where the Dudley's would compete in a losing effort against the Usos. The following night they defeated The Usos in a tables match, breaking their vow to never again use tables and officially ending the feud. Moments afterwards the duo were interrupted by the debuting Enzo Amore and Colin Cassady, who proceeded to insult them and ignite a new feud. In a tournament set up by Shane McMahon to determine the new number 1 contenders to the tag team championships, they would defeat the Lucha Dragons to advance to the semi-finals, where they clashed with Enzo and Cass in a losing effort due to miscommunication between them.