Konnan's first stint with World Championship Wrestling lasted only a few weeks. His debut was at Starrcade on December 16, 1990. Teaming with Rey Mysterio, Sr., Konnan entered the Pat O'Connor Memorial International Cup Tag Team Tournament held at the event. They defeated Norman Smiley and Chris Adams in the quarter-finals, but lost to eventual winners, the Steiner Brothers (Rick and Scott) in the semi-finals. He then won a televised match on WCW Power Hour against Chuck Coates on January 19, 1991.
Konnan received a tryout for the World Wrestling Federation on January 7, 1991 at a WWF Superstars taping in Amarillo, Texas defeating Ultraman. He returned again on March 26 in Las Vegas, Nevada, defeating Louie Spicolli in a WWF Superstars dark match. He would defeat Spicolli again one night later at a Wrestling Challenge taping in Reno. Konnan returned again on January 7, 1992 at a WWF Superstars taping in Daytona Beach, Florida. wrestling this time as The Latin Fury, he defeated The Heartbreaker. The next day he defeated The Juicer in a dark match at a Wrestling Challenge taping in Fort Myers, Florida. Konnan would wrestle twice more as The Latin Fury, the final time at a house show in Hyannis, Massachusetts on July 19, 1992 when he defeated Pete Doherty.
The next day, when he appeared at a WWF Superstars taping in Worcester, Massachusetts against The Mercenary, he was renamed El Relámpago. He wrestled again as El Relámpago the following night against Luis Mendieta.
Konnan made his official WWF debut on September 1, 1992 in Hershey, Pennsylvania during a Superstars taping under the name The Comet Kid when he pinned Barry Horowitz. After three televised matches, Konnan abruptly left the WWF.
Konnan joined Extreme Championship Wrestling (ECW) in 1995 and feuded with The Sandman. He appeared at ECW November to Remember on November 18, 1995, squashing Jason Knight.
Konnan returned to WCW on a full-time basis on the January 22, 1996 edition of Nitro. Promising, in a promo at the start of the show, to defend his "Mexican Heavyweight Championship" against Psicosis the next week. Konnan defeated One Man Gang for the United States Heavyweight Championship on January 29, 1996. He lost the United States Title to Ric Flair on July 7, 1996 at Bash at the Beach, following interference from Flair's valets, Miss Elizabeth and Woman. Several months after losing the United States Championship, Konnan became a villain and joined The Dungeon of Doom. However, the gimmick was already on its way out.
Konnan joined the New World Order (nWo) on July 14, 1997. Konnan developed an increasingly hip-hop based gimmick and was nicknamed "K-Dogg." During his first stint in the nWo, Konnan feuded with the Luchadores of the cruiserweight division. During this storyline, he wrestled in a Mexican Death match at Road Wild against Rey Mysterio, Jr. and a match against Juventud Guerrera at Uncensored in March 1998. When the nWo divided into two rival factions on the May 4, 1998 episode of Nitro, Konnan sided with the nWo Wolfpac, led by Kevin Nash. The Wolfpac feuded with nWo Hollywood, led by Hollywood Hogan and became tweeners. On the November 30, 1998 episode of Nitro, Konnan defeated Chris Jericho for the World Television Championship. His reign lasted until December 28, 1998, when he lost to nWo Hollywood member Scott Steiner on Nitro following interference from Buff Bagwell. When the two halves of the nWo reunited in January 1999, Konnan was thrown out of the nWo for standing up for Rey Misterio, Jr and was attacked by Lex Luger. As a result, he became a face and teamed with Mysterio to fight the nWo. After feuding with nWo member Lex Luger, Konnan and Mysterio, Jr. were defeated by The Outsiders at SuperBrawl IX, with The Outsiders removing Mysterio's mask in the process.
Konnan spent several months feuding with Disco Inferno, and then he began a rivalry with Stevie Ray. He and Mysterio formed an alliance with Master P and his No Limit Soldiers and fought with The West Texas Rednecks. After Master P left WCW, Konnan formed a stable known as The Filthy Animals. He and Mysterio, representing the Filthy Animals, defeated Harlem Heat (Booker T and Stevie Ray) for the WCW World Tag Team Championship on October 18, 1999. They were scheduled to defend the titles against Harlem Heat on October 24, 1999 at Halloween Havoc, but on the night of the event Mysterio was announced as being injured. The title was then contested in a three-way tag match pitting Konnan and Billy Kidman, representing the Filthy Animals, against Harlem Heat and the First Family (Hugh Morrus and Brian Knobs). Harlem Heat regained the title after Stevie Ray pinned Morrus. Konnan and Kidman defeated Harlem Heat for the title the next night on Nitro, but lost to the Harris Brothers (Ron and Don Harris) on November 22, 1999.
Konnan was inactive throughout early 2000, as he was suspended for three months after requesting his release from WCW. Shortly after returning from suspension and reforming the Filthy Animals, Konnan was sidelined once again, this time with a legitimately torn triceps muscle, damaged when Van Hammer threw Juventud Guerrera at him during a match and Guerrera's elbow connected with Konnan's upper arm as he attempted to catch him. Throughout 2000, the Filthy Animals feuded with other stables, including The Misfits In Action, The Natural Born Thrillers and Team Canada. At WCW's final pay-per-view event, Greed, on March 18, 2001, Lance Storm and Mike Awesome (representing Team Canada) defeated Hugh Morrus and Konnan. WCW was sold to the WWF five days later, on March 23.
More than twenty-two years after WWF purchased WCW, which at that point was renamed to the WWE, Konnan made his first WWE programming appearance at the 2023 Hall of Fame, where he inducted his tag team partner and friend, Rey Mysterio.