On the October 27, 2008 episode of "Raw", Punk and Kofi Kingston were able to defeat Cody Rhodes and Ted DiBiase to win the World Tag Team Championship. Punk and Kofi were also members of Team Batista at Survivor Series where they lost to Team Orton. After Survivor Series, Punk entered the number one contender Intercontinental Championship Tournament. Punk was able to defeat Snitsky and John Morrison in the first two rounds. On December 13, 2008, John Morrison and The Miz defeated Punk and Kingston for the World Tag Team Championship at a live event. Punk defeated Rey Mysterio the next day at Armageddon to win the tournament.
On the January 5 episode of "Raw", he received an Intercontinental Championship title match against William Regal. The match ended in a disqualification, when Regal grabbed the referee's shirt. Due to this, Stephanie McMahon gave Punk a rematch the next week. The rematch ended in a disqualification but this time it was Punk that got disqualified. He was awarded another rematch on the January 19 episode of "Raw" but this time it was a No Disqualification match. Punk was able to win the match and the championship. When he won the championship, Punk became the nineteenth Triple Crown Champion. He also became the person to accomplish the Triple Crown in the fastest amount of time, which broke Kevin Nash's old record. On the March 9 episode of "Raw", Punk was defeated for the championship by John "Bradshaw" Layfield. Punk was able to win the Money in the Bank ladder match at WrestleMania XXV and became the first person to win the match twice. At the 2009 WWE Draft on April 13, 2009, he was drafted from "Raw" to "SmackDown". He began a feud with Umaga because of Umaga's multiple surprise attacks when Punk was attempting to cash in his Money in the Bank Contract. The feud resulted in a Samoan strap match at Extreme Rules. The match was won by Punk.
When the pay-per-view was about to end, Punk ran down to the ring, cashed in his Money in the Bank contract and defeated Jeff Hardy to win the World Heavyweight Championship. On the June 15 episode of "Raw", Punk defended his championship in a Triple Threat match against Edge and Hardy. At The Bash, Punk lost to Hardy by disqualification when Punk kicked the referee after he was affected with a storyline eye injury and claimed that he could not see the referee, but because the titles do not change hands from disqualification, Punk retained the championship. When Hardy believed that Punk was faking his eye injury, he called him out on it. This led Punk to turn heel and said that he was the moral superior to fans of Hardy because of his drug-free lifestyle. Punk lost the championship to Hardy at Night of Champions. Punk and Hardy had a Tables, Ladders, and Chairs match at SummerSlam where Punk won the championship back. After the match, Punk was attacked by The Undertaker. Punk's feud with Hardy ended on the August 28 episode of "Friday Night SmackDown" when Punk defeated Hardy in a steel cage match where the loser of the match would have to leave the company. The match earned a Slammy Award for "Shocker of the Year" in 2009.
At Breaking Point in Montreal, Punk competed in a submission match against The Undertaker. Punk defeated The Undertaker in the match to retain the World Heavyweight Championship. The Undertaker originally won the match with his Hell's Gate submission hold. The SmackDown general manager Theodore Long restarted the match after announcing that the ban that the former general manager Vickie Guerrero set on his move was still in effect. Punk won the match with the Anaconda Vise when the referee Scott Armstrong called for the bell even though the Undertaker did not submit (similar to the Montreal Screwjob which happened in the same arena in 1997). Punk was defeated by The Undertaker in a Hell in a Cell match for the World Heavyweight Championship at Hell in a Cell. Punk had a rematch against The Undertaker on "Smackdown" and had another rematch at Bragging Rights in a Fatal Four Way match which also involved Batista and Rey Mysterio but he lost both matches.
He changed his character in a more menacing direction on the November 27 episode of "SmackDown", when he revealed that he had converted Luke Gallows, who had the former gimmick of the mentally incompetent wrestler Festus, to the straight-edge lifestyle which had got rid of his mental problems. He continued to support his straight-edge philosophy, he began to present himself as a cult-like savior to the crowd. He also grew out the hair on his head, face and chest in an allusion to Jesus. Through the month of January, he began to convert planted members of the audience to the straight-edge lifestyle by making them take a pledge of allegiance to him and then shaving their head as a sign of renewal and devotion. After he converted multiple people who were not seen again, one of the converts Serena began accompanying Punk and Gallows and they later formed the Straight Edge Society. While leading the stable, he was also the mentor of "WWE NXT" rookie Darren Young. At one point, Young was going to join the Straight Edge Society but he chose not to join before he was about to have his head shaved.
Punk would occasionally give sermons and even gave sermon while competing in both the Royal Rumble and Elimination Chamber matches. During the Chamber match, Punk was eliminated by Rey Mysterio, who he was feuding with going into the PPV. This raised tensions between the two as Mysterio prevented him from winning a Money in the Bank qualifying match which then lead to Punk interrupting Mysterio's celebration of his daughter's ninth birthday and singing his own version of "Happy Birthday to You" to her. Mysterio challenged Punk to a Street Fight at WrestleMania XXVI but he lost to Gallows. A stipulation was added by Punk that if Mysterio lost, he would have to join the Society. Mysterio defeated Punk at WrestleMania and a rematch took place at Extreme Rules where if Punk lost, he would have to have his head shaved like his disciples. Punk was able to win the match after outside interference from a fourth member of the Society who kept his face covered. A third and final match was held at Over The Limit with both of the previous stipulations put on. At the event, Punk was defeated by Mysterio and had his head shaved bald.
Punk felt embarrassed by having his head shaved and he considered himself to be always pure unlike his followers, Punk appeared under a mask to cover his bald head on the May 29 episode of "SmackDown". At Fatal 4-Way, Punk challenged for the World Heavyweight Championship against Mysterio, The Big Show and the champion Jack Swagger but lost when Kane attacked Punk after Kane accused Punk of being the person who attacked The Undertaker. Punk was unmasked by Big Show on the July 16 episode of "SmackDown" while Punk was healing from an arm injury. On the July 23 episode of "SmackDown", Big Show unmasked the fourth member of the Straight Edge Society and it was revealed to be Joey Mercury. This incident led to a handicap match at SummerSlam. In the match, Big Show defeated the Straight Edge Society when Punk abandoned them. Punk was defeated in a singles match against Big Show at Night of Champions. A little while after, Serena was released from her WWE contract after she reportedly did not "live out" her straight edge persona in public. Mercury had also suffered an injury which caused the group to shorten. Gallows showed signs of dissent and Punk defeated Gallows in a match on the September 24 episode of "SmackDown". The ended the group.