The 42-year-old star was due to appear on the ABC show that is hosted by Michael Strahan - who used to sit alongside Kelly on her morning talk show 'Live!' - but Ryan belatedly decided to back out of his on-screen chat because he knew it would upset Kelly.
An insider explained: ''Ryan was scheduled to be on Wednesday's show well in advance. He's been on the show rundown for a week.
''Then yesterday, or maybe even as late as last night, Kelly threw a s**t fit and told him he couldn't do 'GMA,' so he pulled his appearance.''
Ryan was supposed to appear on the show to promote the new series of 'American Idol', which he will present as it returns to TV screens.
However, Ryan - who now also presents 'Live!' alongside Kelly - performed a last-minute U-turn due to his co-star's ongoing feud with Michael, which stems from him quitting her show without any advance warning in 2016.
The source told the New York Post newspaper's Page Six column: ''It's very clear that Ryan wants to stay on her good side. She's an executive producer on the show, so she has a lot of pull. It's fair to say she has a lot of influence over him. He joined her show. It sounds like she still feels threatened.
''There's still bad blood with Kelly and Strahan, and she doesn't want history to repeat itself and Ryan to be lured to 'GMA' too.''
However, ABC bosses were not too concerned by the last-minute cancellation, because they were still afforded the opportunity to interview the judges, Lionel Richie, Katy Perry and Luke Bryan.
The insider explained: ''Kelly isn't going to be reprimanded for this, as diva-like as it is, because it's not worth upsetting her for a three-minute hit with Ryan on 'GMA.'
''They had the three judges, and the big star Katy Perry, anyway.''