Punk would go to feud with Daniel Bryan starting at Over the Limit when Punk was able to retain his championship after he reversed Bryan's finishing submission hold, the "Yes!" Lock, into a pinning combination. The replay, however, would show that Punk had visibly tapped out moments after the match finished. On the "SmackDown" before the pay-per-view, Bryan would interfere in the non-title match between Punk and Kane to attempt to frame Punk for attacking Kane with a steel chair, which started a three-way rivalry. On the June 1 episode of "SmackDown", a match between Punk and Kane took place for the WWE Championship but it ended in a double disqualification after Bryan ran in and attacked both men. Bryan's ex-girlfriend AJ would turn her affections towards both Punk and Kane. The feud ended when Punk was able to defeat Bryan and Kane in a triple threat match at No Way Out after AJ distracted Kane. Punk was able to defeat Bryan to retain the championship in a No Disqualification match with AJ as the special guest referee at Money in the Bank.
On July 23 episode of "Raw" named "Raw 1000", Punk faced the Money in the Bank winner John Cena and was able to defend his WWE championship but lost the match after Big Show interfered and attack Cena. After the night's special guest The Rock tried to help Cena, Punk would attack him and turn heel. On the next "Raw", Punk would explain that he attacked The Rock because he was tired of being overshadowed by people like Cena and Rock when the main focus of the company should be on the WWE Champion. Punk would attack both Cena and Big Show during their number one contender's match later on in the night. As a result of this, both Cena and Show were put into a title match against Punk at SummerSlam. At SummerSlam, Punk successfully defended his championship against them in a triple threat match. During the following weeks, Punk would demand respect from people like AJ Lee, Jerry Lawler and Bret Hart. He would eventually be managed by Paul Heyman during Punk's feud with Cena. Punk would face Cena to a draw at Night of Champions. Even though Cena was suffering from an arm injury, they continued to feud. Punk would reject Mick Foley and Jim Ross to pick him as his Hell in a Cell opponent and lead to Punk fighting with WWE chairman Vince McMahon. After Cena's injury made him unable to wrestle at Hell in a Cell, he was replaced by Ryback. At Hell in a Cell, Punk was able to defeat Ryback and retain his championship after referee Brad Maddox hit Ryback with a low-blow.
On "Raw" the next night, an angry Mick Foley confronted Punk for not picking John Cena as his Hell in a Cell opponent. Foley and Punk then agreed to face each other in the traditional five-on-five elimination tag team at Survivor Series. Punk would chose Alberto Del Rio, Cody Rhodes, Damien Sandow, and The Miz to be on his team but Punk was later replaced as team captain by Dolph Ziggler after Mr. McMahon booked him in a Triple Threat WWE Championship match against John Cena and Ryback instead. At the pay-per-view, Punk defeated Cena and Ryback after interference from the debuting stable called The Shield (Dean Ambrose, Seth Rollins, and Roman Reigns) which allowed him to retain his WWE Championship. He would hold the championship for a full year. On December 4, Punk underwent surgery for a partially torn meniscus which removed him from his title match against Ryback at . Even though Punk was injured, he became the longest reigning WWE Champion in the past 25 years on December 5, after he reached 381 days which passed John Cena's 380-day reign. Punk returned to in-ring action on the January 7, 2013 episode of "Raw" where he defeated Ryback in a Tables, Ladders, and Chairs match, following interference from The Shield to retain his championship.
Punk defended his WWE Championship against The Rock at the Royal Rumble on January 27, 2013. A stipulation was added to the match where if The Shield interfered, then Punk would be stripped of the title. Punk had originally pinned The Rock to retain his championship after The Shield attacked and put The Rock through a table while the arena lights were out. Vince McMahon came out to the entrance ramp and started to announce that Punk would be stripped of the championship, but he instead restarted the match at The Rock's request. Punk ended up losing the match, ending his record-setting reign at 434 days. Punk would receive a rematch for the championship on February 17 at the Elimination Chamber, with the stipulation that if The Rock was disqualified or counted out, he would lose the WWE Championship. Rock was able to pin and defeat Punk in the match to retain the championship. On the February 25 episode of "Raw", Punk faced off against Royal Rumble winner John Cena for his number one contendership to the WWE Championship, but was defeated.
On January 26, 2014, Punk was the first entrant in the Royal Rumble match. After he was able to last in the match until the final four, Kane, who was already eliminated earlier in by Punk, eliminated Punk from the outside and then chokeslammed him through the announcer's table.
The night after the Royal Rumble, Punk did not show up "Raw" or on the "SmackDown" tapings on Tuesday in Toledo, Ohio even though he was advertised. It was reported by the Wrestling Observer that, on Monday before Raw, Punk legitimately walked out of the company after he told both Vince McMahon and Triple H that he was "going home". On February 20, McMahon said that Punk was "taking a sabbatical" during a conference call to investors. After weeks of hearing the crowd chant for CM Punk at various WWE events, the company decided to make its first comments on the status of Punk on the March 3, 2014 episode of "Raw" in Punk's hometown of Chicago. When the show started, they played Punk's entrance music "Cult of Personality" and his old manager Paul Heyman came out instead. Heyman said that Punk was not at "Raw" and blamed the crowd. He also blamed the Undertaker for Punk's split from Heyman. On July 15, 2014, WWE moved Punk's profile from the active roster to their alumni page without them releasing a statement. On the same day, Punk thanked his fans without mentioning WWE on Twitter. In late July, Punk said that he was "never ever" going to return to wrestling.