As the 1990s began, aging stars gave way to a younger generation including Mitsuharu Misawa, "Dr. Death" Steve Williams, Kenta Kobashi, Gary Albright, Toshiaki Kawada, Mike Barton (Bart Gunn), Akira Taue and Jun Akiyama, leading to perhaps AJPW's most profitable period in the 1990s.

He would then acquire the rights to the company and Baba family stock by early 2003, when another exodus of gaijin wrestlers began, most notably Steve Williams, KroniK (Brian Adams and Bryan Clark), Bill Goldberg and Mike Rotunda.

After Misawa and most of the other wrestlers left the promotion, there was a lull in developing new stars until the likes of KAI, Suwama, Hama and T28 debuted from the mid-2000s onward and helped restrengthen the company.

With established stars such as Keiji Muto, Satoshi Kojima, John "Earthquake" Tenta, Masakatsu Funaki, D'Lo Brown and Minoru Suzuki anchoring the promotion, the younger wrestlers were given time to grow and by 2010 were set to help lead All Japan.

Gaijins who signed with AJPW full-time were given pushes regardless of which promotion they arrived, most notably Stan Hansen, "Dr. Death" Steve Williams, Gary Albright, Vader and Mike Barton.

[3] The January 28, 2001 pay-per-view was All Japan's second highest attendance of all time at 58,700,[4] which was notable for Stan Hansen's retirement and the Steve Williams vs. Mike Barton Brawl For All revenge angle.

[5] In April 1990, Genichiro Tenryu led the first exodus of wrestlers (The Great Kabuki, Samson Fuyuki, Tatsumi Kitahara, Masao Orihara, Yoshiaki Yatsu, Goro Tsurumi, and Shinichi Nakano) lured as they were to form Super World of Sports, which enabled Baba to push Misawa, Kawada, Taue and Kobashi to be his new stars.

Not wanting to choose sides, Johnny Ace would retire from active competition and return to World Championship Wrestling in the United States as a road agent.

On June 16, 2000, 24 out of the 26 contracted native wrestlers for All Japan were led by Misawa for a press conference, where it was announced that they would be leaving the promotion (Masanobu Fuchi and Toshiaki Kawada remained).

Misawa was interviewed in Tokyo on June 21, where he announced that he and the other wrestlers leaving to form Noah would compete on four of the sixteen shows in All Japan's Summer Action Series 2000 tour, which began on July 1.

On June 28, 2000, Misawa formally announced at a press conference that Pro Wrestling Noah would debut with two consecutive shows (titled "Departure") in Differ Ariake on August 5 and 6 in Tokyo.

On July 20, 2000, Yoshinobu Kanemaru, Takeshi Morishima, Naomichi Marufuji, Kentaro Shiga, Takeshi Rikio, Mitsuo Momota, Rusher Kimura, Haruka Eigen, Tsuyoshi Kikuchi, Kenta Kobayashi, Takao Omori, Yoshihiro Takayama, Jun Izumida, Masao Inoue, Yoshinari Ogawa, Akira Taue, Jun Akiyama and Mitsuharu Misawa competed in their last matches for All Japan Pro Wrestling at the sold out Hakata Star Lane in Fukuoka.

Mrs. Baba appointed Stan Hansen as the new Chairman of All Japan's Pacific Wrestling Federation title governing body, replacing Lord James Blears.

In response, New Japan foreman Riki Choshu rushed into the ring and exchanged a firm handshake with Fuchi, signaling the beginning of the cross-promotional alliance.

[6] In 2001, Keiji Muto and Shinjiro Otani created the interpromotional stable BATT (Bad Ass Translate Trading), which included All Japan's Taiyō Kea, Michinoku Pro's Jinsei Shinzaki and Hiroshi Hase.

A notable shift in the product was seen in July 2001, when in a pay-per-view main event, Steve Williams lost to Keiji Muto for the Triple Crown Heavyweight Championship, where it ended in an altercation.

[7] 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.

Muto upheld some traditional aspects of the Baba-run All Japan, as the Champion Carnival and World's Strongest Tag Determination League remained annual events.

Instead, shares of All Japan were sold to Gaora TV with the promotion still operating in its usual corporate manner led by Keiji Muto, rarely broadcasting pay-per-views to SKY PerfecTV!

After Mrs. Baba sold the company, gradually over time All Japan took a more sports-entertainment based approach, featuring more in-ring promos, comedy segments, and gimmick matches.

After John Tenta left All Japan in July 2003 and Jerry Tuite's death in December, who often tag-teamed with each other to fight Keiji Muto's posse, Jamal (Umaga) and Taiyō Kea would take the roll as the top gaijins in the mid-2000s.

[21] Keiji Muto competed at a Pro Wrestling Noah event on July 10, 2004, teaming with fellow AJPW wrestler Taiyō Kea to face Mitsuharu Misawa and Yoshinari Ogawa.

Kea defeated Toshiyaki Kawada for the Triple Crown Heavyweight Champion on the August 27, 2006 pay-per-view,[23] before losing it to up-and-comer Minoru Suzuki a week later on the September 3, 2006 edition of AJPW TV.

[12][36][37] In the weeks that followed, Masakatsu Funaki, Kaz Hayashi, Shuji Kondo, Ryota Hama, Masayuki Kono, Hiroshi Yamato, Koji Kanemoto, Minoru Tanaka, Yasufumi Nakanoue, Kai, Seiya Sanada and Andy Wu announced their resignation from the promotion out of loyalty to Muto.

[48] After the exodus (along with the departures of ring announcer Makoto Abe and referees Daichi Murayama and Daisuke Kanbayashi), the promotion has now been reduced to less than half the active roster.

[49] On July 5, 2013, all five members of Burning (Akiyama, Shiozaki, Aoki, Suzuki, and Kanemaru) officially signed exclusive contracts with AJPW, ending their tenure as freelancers, along with the returns of Taiyo Kea and referee Kyohei Wada.

[50][51] On July 14, during the launching event of the post-Muto All Japan, Masanobu Fuchi announced that he had officially re-signed with the promotion not only as a wrestler, but also as a member of the Board of Directors, ending his tenure as a freelancer.

[74] On November 27, 2016, the promotion returned to Ryōgoku Kokugikan for its first event at the venue in three years, headlined by Kento Miyahara defending the Triple Crown Heavyweight Championship against Suwama.

On May 7, 2021, the Japanese government announced an extension to the state of emergency currently in place in Tokyo and other prefectures, leading AJPW to postpone their event on May 15 at Ota City General Gymnasium to June 26.

On July 12, 2022, it was announced that AJPW would be celebrating its 50th anniversary event on September 18, 2022, at the Nippon Budokan, marking the return of the promotion to the arena for the first time in eighteen years.