In the fall of 1988, Muto moved to the Dallas, Texas-based World Class Championship Wrestling, where he reunited with Kendo Nagasaki and had a feud with Kevin Von Erich before departing the organization in March 1989.

Later that year, Muto and Chono, along with Hashimoto, cemented their status as the next generation of New Japan, surpassing Antonio Inoki, Tatsumi Fujinami, and Riki Choshu, after the finals of the first G1 Climax tournament on August 11.

In October, Muto paired with Hiroshi Hase to participate in the 1991 Super Tag League, where they lost three of their tournament matches and won three, narrowly missing the chance to qualify for the knockout stage.

However, shortly after the tournament, the duo found success as they defeated Rick Steiner and Scott Norton to win the IWGP Tag Team Championship at Budokan Hall on November 5.

In the process, Muto began teasing at a possible turn to the side of the nWo, proclaiming himself to be the true successor to Antonio Inoki's legacy, and "accidentally" attacking his own partners in the middle of a match.

During this period, Muto underwent a long slump in big matches, losing not only to members of the nWo, but fellow New Japan wrestlers including Power Warrior at Wrestling World on January 4, 1997, and Shinya Hashimoto for the IWGP Heavyweight Championship on June 5.

Muto would then team with teammate Satoshi Kojima as they won the Super Grade Tag League by defeating Shinya Hashimoto and Tatsumi Fujinami in the final on December 6.

Muto successfully defended the IWGP Heavyweight Championship against Kensuke Sasaki at St. Valentine's Day Massacre, Team 2000 member Don Frye at Strong Style Symphony, Genichiro Tenryu on May 5 and Satoshi Kojima on July 20.

The following month, Muto entered the Super Grade Tag League with stablemate Scott Norton, which they won by defeating Manabu Nakanishi and Yuji Nagata in the final.

Muto took an extended hiatus to rehabilitate his damaged knees after that, focusing instead on one last run in America for WCW, thus marking the dissolution of nWo Japan as it merged into Chono's Team 2000.

After a planned tag team match with FMW's Hayabusa for Wrestling World 2001 was cancelled due to Hayabusa's injury to both his elbows that required reconstructive surgery, it seemed as if Muto reached a confusing crossroads in his career; however, he chose to completely change his image, shaving his head bald (he had a pronounced receding hairline throughout much of 2000), growing out a goatee, and aligning himself with a fellow NJPW wrestler who had gone overseas for an extended period of time, Shinjiro Otani.

Muto then entered the 2001 G1 Climax, where he won all matches in his block, with the exception of a loss to Satoshi Kojima, thus qualifying for the semi-final on August 11, in which he defeated Tadao Yasuda and then lost to Yuji Nagata in the final a day later.

Muto captured more gold by winning All Japan's World Tag Team Championship alongside stablemate Taiyō Kea by defeating Genichiro Tenryu and Yoji Anjo on October 22.

At Clash of the Champions XIII in November 1990, it was announced that The Great Muta would be returning to World Championship Wrestling at Starrcade '90: Collision Course the following month to team with Mr. Saito.

On January 11, 2002, following the end of a year-long cross-promotional angle with New Japan Pro-Wrestling, Keiji Muto shocked the Japanese wrestling world by defecting to All-Japan as a full-time competitor, taking Satoshi Kojima and Kendo Kashin with him.

In his first match as an AJPW contracted wrestler, Muto and Taiyo Kea successfully defended the World Tag Team Championship against Mike Barton and Jim Steele on January 14.

Three days later, at Grand Champion Carnival, Muto faced Genichiro Tenryu in a match for the vacant Triple Crown Heavyweight Championship after Kawada was forced to vacate the title due to injury.

On December 27, Muto made a return to the United States, wrestling for the Ring of Honor promotion as part of an interpromotional All Japan vs. ROH card, which hosted a series of cross-promotional "dream" matches.

In the fall of the year, Muto and his partner Joe Doering participated in the 2007 Real World Tag League, which they won by defeating Satoshi Kojima and Suwama in the final on December 9.

Muto had won the IWGP Heavyweight Championship in NJPW earlier in 2008 and successfully defended the title in All Japan against Hirooki Goto at Pro-Wrestling Love in Ryogoku Vol.

He then appeared at Wrestle Kingdom I in 2007 where he reunited with former partner and rival Masahiro Chono to defeat Tencozy in a "Super Dream Tag match" pitting NJPW and AJPW wrestlers together.

[30] After the match, Muto said backstage that he had passed Tanahashi his sash after doing his best for over half a year to raise the worth of the title, and suggested that he would withdraw and leave New Japan to move their company forward.

[32] Muto returned to New Japan again a year later at Wrestle Kingdom 8 in Tokyo Dome, now working as The Great Muta in a tag team match, where he and Toru Yano defeated Suzuki-gun (Minoru Suzuki and Shelton X Benjamin).

On January 4, 2023, at Wrestle Kingdom 17 night 1, Muto competed in his final NJPW match, teaming with Hiroshi Tanahashi and Shota Umino to defeat Los Ingobernables de Japon (Tetsuya Naito, Sanada and Bushi).

In 2007, while Muto was in Orlando, Florida, in order to establish a working agreement between All Japan and Total Nonstop Action Wrestling (TNA), he made an appearance for the company, under his Great Muta gimmick, at the Destination X pay-per-view, in a segment with Christian Cage.

[55] On April 1, 2020, at Wrestle-1's final event, Muto team with Kaz Hayashi, Masayuki Kono, and Shuji Kondo unsuccessfully against Kuma Arashi, Shotaro Ashino, Daiki Inaba, and Koji Doi.

On November 9, 2019, Muto made a surprise special appearance at All Elite Wrestling's Full Gear as one of the judges for the AEW World Championship match, in the event of a draw.

In 1995, Muto starred in the Japanese thriller Yajuu Densetsu: Dragon Blue, as Ryusaki, a suave detective who joins forces with a beautiful young spiritualist named Mazuki (played by Hiroko Tanaka) to solve a bizarre case of killings from a mystical sea creature.

Muto has worked extensively with Japanese clothing company A Bathing Ape, helping them to produce a number of t-shirts featuring his likeness and the All Japan Pro Wrestling logo.

[79] Muto appears as a gang member in the 2017 video game Yakuza Kiwami 2, alongside Genichiro Tenryu, Masahiro Chono, Riki Choshu and Tatsumi Fujinami.