The Coach made a heel turn against Shane McMahon on August 24, 2003 at SummerSlam. After this he would have an on-screen role as the "lackey" to then General Manager of Raw, Eric Bischoff. Coachman continued to work as a heel and later teamed up with his fellow WWE Heat announcer Al Snow in a storyline feud against the Raw announce team, Jerry Lawler and Jim Ross. This feud would even see the pair win the right to announce the main show from the Ross and Lawler at one point. Later, Coachman achieved a singles victory on pay-per-view at Backlash, in 2004 by defeating Tajiri (albeit with the assistance of Garrison Cade). Coachman would go on to host the 2004 and 2005 Raw Diva Searches. Later, Coach would gain his own column in the now defunct Raw Magazine ("Coach's Corner") and his own webcast on WWE.com ("CoachCast"). Coachman was officially added as the third member to the Raw broadcast team and signed a multi-year contract with WWE in 2005.
During October 2005, Coach was involved in an angle involving the McMahon Family publicly firing Jim Ross due to the actions of Ross's friend, Steve Austin. The firing of Ross gave Coach the position of lead announcer on Raw. The storyline would culminate in a match at Taboo Tuesday where Austin faced Coach in a match with both Austin's and Ross's jobs on the line. Though the match was originally scheduled to be Austin versus the Coach, Austin refused to participate because of issues he had with the storyline (the original story is said to have called for Austin to lose following a run-in by the returning Mark Henry). World Heavyweight Champion Batista was renamed the opponent to play up the SmackDown! vs. Raw storylines. On the October 31, 2005 edition of Raw, Batista came out and accepted the match only to be attacked by Coach's backup, the returning Goldust and Vader. At Taboo Tuesday, Batista faced off against Coach in a Street Fight. Vader and Goldust tried to interfere in the match, but Batista won. However, no mention of the Jim Ross stipulation was ever mentioned after the match.
Former ECW announcer Joey Styles soon replaced Coach in a move that became permanent despite Coach's on-air protestations that Styles' presence was temporary. Coach retained a prominent role on the Raw announcing team as the heel representative of a three-man booth with Styles, the play-by-play man, and Jerry "The King" Lawler, the babyface color commentator.
On the January 23, 2006 edition of Raw, Coach defeated Lawler to win the last Raw spot in the Royal Rumble match via interference from the debuting Spirit Squad. Coachman would enter seventh during the match only to be eliminated almost immediately by The Big Show.
During the April 24 edition of Raw, after Coachman hosted a Divas bikini contest, Viscera would come down to the ring and perform the Viscagra on Coachman. During the commercial break of that show, still in the ring, he quit in protest of his treatment on Raw. On the May 5 edition of Heat, broadcast partner Todd Grisham announced that Coachman had quit, saying, "We've got announcers quitting left and right. It was Coach two weeks ago, Joey Styles this past week." On the May 29 edition of Raw, it was revealed that Mr. McMahon had hired Jonathan Coachman under the new position of McMahon's Executive Assistant; to aid McMahon in the daily running of the Raw brand, and actually acted as the General Manager when the McMahons were absent. While Executive Assistant, Coachman, along with the McMahons, would feud with the reformed D-Generation X, and also have issues with John Cena. On June 18, 2007, Coachman was officially named Interim General Manager of Raw by the McMahon Family following the kayfabe death of Vince McMahon in a limo explosion.
On the August 6, 2007 edition of Raw, William Regal became the new General Manager on the Raw brand after winning an battle royal featuring other participants from the Raw roster. As a result, Coachman was removed from his position as Interim General Manager and became Regal's new assistant. However, following a vicious kayfabe assault by John Cena on Regal during the September 3 edition of Raw, Regal had to be temporarily relieved of his duties as General Manager at which point Coachman was once again named interim General Manager of Raw until Regal was fit to resume his role. On the October 1 edition of Raw, Regal returned as General Manager which resulted in Coachman being once again demoted to his prior rank.
On the December 3, 2007 edition of Raw, Coach was in a No DQ Handicap match with Carlito against Hornswoggle, with whom he had been having problems. However, Hornswoggle had paid the APA to protect him during the match. Coachman ended up being pinned by Hornswoggle after a Clothesline From Hell and a Tadpole Splash.
A rivalry ensued, and during it, another Hornswoggle trap style event occurred. One night Coachman chased Hornswoggle all over the backstage area, and it eventually moved to the arena, where Hornswoggle performed his infamous "hide under the ring" trick to get away. Coachman moved to the other side of the ring and pulled out a detonator, much to the surprise of Jim Ross. He attempted to detonate the detonator twice, but nothing happened. He then moved under the ring to check the explosives, and Hornswoggle came out from under the ring, and deteonated successfully, causing smoke to appear from under the ring.
Coachman became Michael Cole's new SmackDown! broadcast partner on January 4, 2008 (after John "Bradshaw" Layfield had left the position to return to the ring). He was replaced by Mick Foley, however, at Backlash on April 27, due to him leaving the WWE.
On March 25, 2016, Coachman made a special appearance during WWE's live event held at Madison Square Garden. On the March 28 episode of Raw, Coachman returned to WWE TV in almost 8 years, cutting a promo with The New Day. Coachman would also announce that SportsCenter would be live leading up to WrestleMania 32 on April 3.