In 1994, Malenko joined Extreme Championship Wrestling (ECW) on August 27, 1994, as a heel participating in a tournament for the vacant ECW World Heavyweight Championship. He defeated Osamu Nishimura in the quarterfinals before he ended up losing to the eventual winner Shane Douglas in the semifinals. Malenko became known as "The Shooter". On November 4, 1994, he defeated 2 Cold Scorpio to win his first ECW Television Championship.
In the beginning of 1995, Malenko formed a faction called the Triple Threat with Chris Benoit and Shane Douglas. On February 25, 1995, Benoit and Malenko defeated Sabu and the Tazmaniac for the ECW Tag Team Championship, making Malenko a double champion. A month later, Malenko dropped the Television Title to 2 Cold Scorpio. On April 8, he and Benoit lost the tag titles to The Public Enemy (Johnny Grunge and Rocco Rock).
In the summer of 1995, Malenko feuded with TV Champion Eddie Guerrero, culminating in a match on July 21 where Malenko defeated Guerrero to win his second ECW Television Championship. Only a week later, Malenko dropped the title back to Guerrero. The two continued to battle over the Television Title and fought a series of matches. His last ECW match was a two out of three falls match against Guerrero, which took place on August 26. The match ended in a draw as the last fall had both men's shoulders on the mat. This would be both men's last match in ECW and they both gave—and received—an emotional farewell to the fans.
In September 1995, Malenko and Benoit joined World Championship Wrestling (WCW), where he continued to be a villain. Malenko came to be known in WCW as "The Iceman" Dean Malenko because of his cold, calculating demeanor and was also given the nickname of "The Man of 1,000 Holds". On May 2, 1996, Malenko defeated Shinjiro Otani for the WCW Cruiserweight Championship in Orlando. He held the title for two months, making successful defenses against the likes of Brad Armstrong, Rey Mysterio, Jr., and Disco Inferno before losing the title to Mysterio on the July, 8 edition of Nitro. He defeated Mysterio Jr. for his second WCW Cruiserweight Championship at Halloween Havoc 1996.
After a successful title defense against Psychosis at World War 3, Malenko lost the Cruiserweight title to Último Dragón at Starrcade. Malenko defeated Dragón on the January 22, 1997 Clash of the Champions XXXIV to win his third WCW Cruiserweight Championship. He would hold the belt for nearly a month before losing it to Syxx at SuperBrawl VII. Malenko lost the match after Eddie Guerrero inadvertently caused Malenko to be hit with Guerrero's United States Title belt.
Malenko then entered a feud with Guerrero, angry over the fact that he had caused him to lose his Cruiserweight belt, and began to attempt to win the United States title from him. The match between the two took place at Uncensored the next month and interference from Syxx played a role again. The Cruiserweight Champion again tried to take Guerrero's title, but in the process dropped the camcorder he carried to the ring with him. After Guerrero took the belt back, Malenko hit him in the back of the head with the camcorder and knocked the champion out, enabling him to pin Guerrero and win his first United States Championship. He retained the belt at Slamboree on May 18, 1997 by defeating Jeff Jarrett, but lost the title to him on the June 9, 1997 episode of Nitro.
At World War 3, Malenko participated in a 60-man, three-ring battle royal won by The Giant. At Starrcade 1997, he challenged Guerrero for the Cruiserweight Title but ended up losing the match. In mid-1998, Malenko engaged in a heated feud with Chris Jericho. To better Malenko's claims, Jericho boasted that he was "The Man of 1,004 Holds" and the two had a final showdown at Uncensored 1998 for the Cruiserweight title. After a long match, Jericho forced Malenko to submit in an angled Liontamer. After the match, the otherwise collected Malenko was left in an unusual fit of frustration. Gene Okerlund then confronted Malenko post match, aggressively citing his many losses in the past several months and asking where he would go from this point. Dejected and worn down, Malenko replied simply, "Home," and would not be seen on WCW television for two months. In the ensuing two months, Jericho proceeded to mercilessly taunt Malenko, including insulting Malenko's father and attacking Malenko's brother.
At Slamboree 1998, Jericho held a battle royal for a shot at his Cruiserweight Championship. Malenko entered the battle royal dressed as masked wrestler Ciclope and won the match, after Juventud Guerrera shook his hand, and eliminated himself. He then unmasked, revealing himself to the crowd following his win. Malenko went on to defeat Jericho for his fourth and final WCW Cruiserweight Championship, thus becoming the first-ever wrestler to win the Cruiserweight title four times. Malenko was stripped of the title, however, as he did not earn the title shot as himself. At The Great American Bash 1998, Malenko and Jericho faced each other in a match for the vacant Cruiserweight title. Malenko lost by disqualification, making Jericho the champion. At Bash at the Beach 1998, Malenko interfered in Jericho's title defense against Rey Mysterio, Jr., allowing Mysterio to pin Jericho for the title. The title was returned to Jericho, however, because of interference by Malenko. Malenko was fired in storyline, but returned at Road Wild 1998 as the special guest referee during Jericho's defense against Juventud Guerrera. Juventud won the match and the title.
In September 1998, Malenko became a part of the final incarnation of Ric Flair's Four Horsemen faction. They feuded with the New World Order (nWo), particularly Eric Bischoff. Malenko and Benoit also battled The West Texas Rednecks (Curt Hennig and Barry Windham) during this period. At SuperBrawl IX, they lost to the Rednecks in the finals of a tag team tournament for the vacant WCW World Tag Team Championship. At Uncensored 1999, however, they defeated the Rednecks in a lumberjack match to win the WCW World Tag Team Championship. Two weeks later, they lost the titles to Rey Mysterio, Jr. and Billy Kidman.
After the Horsemen were finally disbanded in May 1999 due to Flair's abuse of power, Malenko joined up with Shane Douglas' faction, The Revolution, which was formed in July 1999. They feuded with David Flair, Diamond Dallas Page and Chris Kanyon. At Bash at the Beach, Malenko challenged David Flair for the U.S. title, but lost the match. They battled many teams throughout the year including West Texas Rednecks, the First Family, The Filthy Animals and The Varsity Club. Malenko's last WCW match was a "catch-as-catch-can" match with Billy Kidman at Souled Out. Early on, Malenko instinctively left the ring to regroup and was disqualified under the match stipulations because his feet hit the arena floor.
After being granted his release from WCW the night after his last WCW match, Malenko signed with the World Wrestling Federation (WWF) and debuted on January 31, 2000 edition of Raw is War. Malenko first appeared in the crowd with the infamous Radicalz – himself, Eddie Guerrero, Chris Benoit, and Perry Saturn – who all made exits from WCW at the same time. While not having as much success in the WWF, Malenko was a force in the promotion's light heavyweight division. Along with Guerrero, Benoit, and Saturn, he had some measure of success as part of The Radicalz. On the March 13 edition of Raw is War, Malenko defeated Essa Rios for his first Light Heavyweight Championship. In April 2000, he feuded with Scotty 2 Hotty who was the new challenger for his Light Heavyweight title. He dropped the title to Scotty on the April 17 edition of Raw is War before he won his second WWF Light Heavyweight Championship from Scotty on the April 27 episode of SmackDown!. At Backlash, Malenko successfully defended the title against Scotty, thus ending the feud between the two.
Later that year, with Benoit having drifted away from the group, Malenko engaged in a feud with Guerrero and Saturn which stemmed from Guerrero's on-screen relationship with Chyna and a number of losses suffered when working as a tag team with Saturn. The feud led to a triple threat match at Judgment Day, where Guerrero retained the WWF European Championship against both Malenko and Saturn. After a brief absence from television, Malenko returned to reform The Radicalz with Guerrero, Benoit, and Saturn. Around this time, Malenko briefly became known as "Double Ho Seven". The gimmick was born out of a match with The Godfather, who offered one of his female escorts to Malenko instead of wrestling him. Malenko gladly accepted his opponent's offer. As Double Ho Seven, Malenko competed for the affections of Lita and feuded with her tag team the Hardy Boyz. He even offered Lita a title match for his Light Heavyweight Championship, but under the condition that if she lost she would be obliged to go on a date with him. Lita accepted and almost caught Malenko by a few nearfalls throughout the match, but in the end lost the match by submitting to his signature Cloverleaf.
Malenko's feud with the Hardy Boyz and Lita continued in early 2001, culminating with Lita pinning him (with some assistance from Matt Hardy) in a match on the February 19, 2001 edition of Raw is War. He also briefly feuded with Jacqueline and Ivory, who were disgusted by his lecherous ways. A title feud with Crash Holly would begin after Crash interfered in a two-on-one intergender handicap match between Malenko, and both Jacqueline and Ivory, costing him the match. After both Guerrero and Benoit drifted away from the Radicalz, Malenko teamed with Saturn for a few weeks before quietly disappearing off television as the WCW/ECW Invasion storyline began in summer 2001.
Malenko appeared in the ring along with other WWE alumni during a segment of the WWE Homecoming edition of Raw on October 3, 2005.
His close friend Eddie Guerrero died on November 13, 2005 and Malenko made a special appearance on the November 14 edition of Raw alongside Chris Benoit. The following Friday on SmackDown!, Malenko once again appeared after a match between Chris Benoit and Triple H, and the three embraced. After the 2006 Royal Rumble, he was seen congratulating Rey Mysterio on his Rumble victory. At Vengeance 2007, he appeared in a backstage segment watching Chavo Guerrero. On the Chris Benoit memorial episode of Monday Night Raw, he talked about the life of Chris Benoit.
On February 27, 2007, Místico defeated Malenko in a tryout dark match before a television taping in San Jose, California. Malenko then appeared on the March 31, 2008 episode of Raw to join The Four Horsemen and other WWE superstars in a farewell tribute to Ric Flair. He made an appearance on the June 28, 2010 episode of Raw congratulating Ricky Steamboat on his DVD release. He and all the others in the ring were attacked by the Nexus. Malenko appeared along the rest of the WWE roster after the April 23, 2012 episode of Raw to celebrate John Cena's 35th birthday. On the September 11, 2017 episode of Raw, Malenko made a brief backstage appearance alongside Jamie Noble, where the two were seen as possible choices by Raw Tag Team Champions Seth Rollins and Dean Ambrose as their partners for an eight-man tag-team match, but were quickly dismissed. On the June 5, 2018 episode of SmackDown Live, Malenko appeared during the contract signing between AJ Styles and Shinsuke Nakamura.
On April 26, 2019, Malenko was released from his producers contract with WWE.