In January of 2002, Keiji Mutoh shocked the puroresu world when he announced he was leaving New Japan for All Japan, and bringing young star Satoshi Kojima with him (Kendo Kashin came as well). The reasons were multi-fold. One of the big reasons was that Mutoh didn't like the direction of New Japan, which was going in an MMA direction that a lot of the purist didn't think was the right way to go. At 39, Mutoh clearly wasn't in any condition to start wrestling like an MMA fighter, and he knew he wouldn't be as big a part in the promotion as those that were able and willing to wrestle in that style. Another big reason is that Mutoh was offered the President position at All Japan, and he got the blessing from Motoko Baba to run the promotion as he wished. This was huge on a number of levels, as All Japan had been struggling since Misawa had formed NOAH in 2000 (taking most of All Japan's wrestlers with him) and many had thought All Japan would soon close. The promotion still was in financial straits but adding Mutoh and Kojima to the mix helped boost the promotion's popularity.

Mutoh wasted no time making an impact as he won the Champion Carnival in March, becoming the first wrestler to win both the G1 Climax and the Champion Carnival. A month prior, Mutoh lost the Triple Crown to Toshiaki Kawada, but after Kawada was injured the title was held up. Mutoh met Tenryu in the Decision Match for the Triple Crown Championship on April 13th, 2002, but Tenryu would win the title for the third time. While in the ring Mutoh was doing well, some of his out of the ring decisions were drawing questionable looks from many fans. This was the first time Mutoh had control over a promotion and there were certainly some growing pains. The biggest example of Mutoh making mistakes is when he brought in Bill Goldberg in August of 2002, and had him squash both Kojima and Kea in under five minutes. This was after Kea had picked up a big win over Tenryu in July. Of course, neither wrestler got anything back for their loss, and the idea that Mutoh spent tens of thousands of dollars to bring over Goldberg to squash two rising stars of the promotion for no reason raised the anger of a lot of fans, some of which still are angry about it to this day. But it didn't do any long term damage as Goldberg had been built up as a monster, it just did nothing to help the promotion and was a financial failure. Another poor decision was Mutoh co-promoting the Wrestle-1 event in January of 2003, which bombed at the Tokyo Dome. Since 2003 however things got better and by 2005 Mutoh was making much better booking decisions bringing in wrestlers and the promotion began turning it around.

Back in the ring, on October 27th, 2002, as the Great Muta he would avenge his loss earlier to Tenryu and win the Triple Crown. Mutoh had debuted the new version of the Great Muta character in July against Kojima, as since Mutoh went through a transformation the Great Muta had to as well. He wouldn't hold it for long however as on February 23rd his old nemesis Shinya Hashimoto invaded the promotion and won the Triple Crown! Mutoh wouldn't get another title shot until late 2005, as he began focusing on tag team wrestling. He began teaming with Arashi in 2003 and on June 8th they won the All Japan World Tag Team Championship. They made five successful defenses of the titles (including a defense in Ring of Honor) before losing the titles to Satoshi Kojima and Kaz Hayashi in early 2004.

After not doing so well the previous year, in 2004 Keiji Mutoh won the Champion Carnival for the 2nd time. Mutoh wrestled for many different promotions in 2004, including a match in New Japan, Zero One, and NOAH. In NOAH, he teamed with Kea to take on Misawa and Ogawa, the first time ever that Misawa and Mutoh had been in the same ring together. They would team in October on Mutoh's 20th Anniversary event, but that would be the last time they wrestled in the same match together before Misawa's unexpected death in June of 2009. In the fall, a new GREAT MUTA challenged Mutoh, which lead to Demon Muta taking down the imposter in December. In 2005, Mutoh finally got another shot at the Triple Crown in July against Kojima, but Mutoh fell to the lariat. He tried again as Great Muta in March of 2006, but with the same result. In both 2005 and 2006 Mutoh didn't do too well in the Champion Carnival. The Great Muta was taking part in the W-1 Grand Prix 2005 tournament and defeated both Akebono and Kensuke Sasaki, but the promotion disbanded before the tournament was finished. In the 2005 Real World Tag League Mutoh teamed with Akebono, but they lost in the Finals to Team 3-D.

As 2007 began, Mutoh certainly appeared to be in the twilight of his career as it had been four years since he held a singles title. At the New Japan Tokyo Dome in January, as part of a Hashimoto Tribute, Mutoh returned to team with Chono as they defeated Tenzan and Kojima. Mutoh proved to everyone he wasn't done yet when he won the Champion Carnival in 2007, which gave him a shot at the Triple Crown against the invading Minoru Suzuki. They finally met in July, with Mutoh threatening to use the Original Shining Wizard, but Suzuki won with a Heel Hold. The success of the promotion and the joining of sponsors allowed All Japan to enter Sumo Hall once again, and on both shows in 2007 the Great Muta teamed with Tajiri to win their matches. In the Real World Tag League, Mutoh teamed with new wrestler Joe Doering and together they won the tournament (the 2nd time for Mutoh). During the first tour in January of 2008, Doering and Mutoh won the All Japan World Tag Team Championship, Mutoh's first championship in four years.

As great of a career Mutoh had had up to this point, 2008 turned out to be one of the best years of his career. Suffering permanent knee damage but missing no time since joining All Japan, Mutoh was hobbled but still defiant as he continued winning matches. After defeated Hirooki Goto in New Japan as the Great Muta at the January Tokyo Dome show, on April 27th, 2008 as Keiji Mutoh he challenged Shinsuke Nakamura for the IWGP Heavyweight Championship. No one thought he was going to win, but with the New Japan crowd solidly behind him Mutoh showed that he wasn't ready to be put out to pasture and stunned the young New Japan star, winning with the moonsault! Mutoh held the IWGP Heavyweight Champion for the rest of the year, defeating Nakanishi, Goto, and Makabe along the way. On September 28th, 2008 as Great Muta he challenged Suwama for the Triple Crown and won, making him only the 2nd wrestler to have both major titles at the same time (sadly he had lost the All Japan World Heavyweight Tag Team Championship prior to that, otherwise he would have had seven belts to beat his old record of six). Ending the year Mutoh still held both major titles and was named Tokyo Sports Wrestler of the Year. Even though he was 45 years old he still captivated and entertained like no other and showed that brains and charisma can make up for any physical limitations. He lost the IWGP Heavyweight Championship in the main event of the Tokyo Dome to Hiroshi Tanahashi, in front of the biggest crowd that New Japan had gathered in years, a fitting end to the storyline as he finally loses to his young protege. Mutoh continues to lead All Japan both out of the ring and in the ring today, and there is no doubt he will continue adding to his legendary and Hall of Fame career for many years to come.