"I said, 'Listen, not one person is going to a movie where the lead character dies from Aids and then you carry on to see how the band carries on'."
During his chat with Stern, Baron Cohen called Queen's lead guitarist Brian May an "amazing musician" but "not a great movie producer".
Last year Queen drummer Roger Taylor gave Britain's Independent newspaper another reason why Baron Cohen departed which included that he "wasn't really at heart an actor".
"We didn't really feel in the end that he (Baron Cohen) was right. We wanted an amazingly good actor in the purest sense."
May also told Classic Rock magazine that "in the end we felt that his presence in the movie would be very distracting".
Baron Cohen says the band has some great stories to tell about their opulent lifestyle but he regrets not walking away sooner.
"There are amazing stories about Freddie Mercury," he told Stern.
"The guy was wild. There are stories of little people with plates of cocaine on their heads walking around a party.
"Apparently, the band nixed the idea of telling those grittier stories.
"They wanted to protect their legacy as a band."
- Bang! Showbiz