The Gone Girl star appeared on Real Time With Bill Maher Friday evening where he quickly got into a disagreement about Islam with the host and other panelists including author Sam Harris.
During the debate, Affleck felt Maher and Harris were presenting an overly broad and negative picture of those who practice Islam.
"We can criticize Christians…but when you want to talk about the treatment of women, homosexuals and free thinkers in the Muslim world, liberals have failed us. The crucial point of confusion is we have been sold this meme of Islamaphobia –where every criticism of the doctrine of Islam gets conflated with bigotry towards Muslims as people, which is intellectually ridiculous."
Affleck, who believes the minority of radical Islamists shouldn't give a bad name to the majority of Muslims who do not share the same views, couldn't help but step in and voice his opinion.
PHOTOS: Ben Affleck's biggest movie roles
Harris wouldn't back down and called Islam "the motherload of bad ideas." Affleck responded saying, "It's just an ugly thing to say."
Maher went further and compared Islam to the mafia.
"It's the only religion that acts like the mafia," he explained. "That will f--king kill you if you say the wrong thing, draw the wrong picture, or write the wrong book."
PHOTOS: Hollywood's democrats revealed
"What is your solution? That we condemn Islam?" Affleck responded before the group finally agreed to disagree. Watch the full debate in the video above.
Affleck has been involved with politics for many years. In fact, his activism sparked rumors of a senate run in 2012.
More recently, the Hollywood A-lister made waves in Washington when he testified before a Senate panel in support of the Democratic Republic of Congo. He would quickly earn the respect of then-Senator John Kerry.