Moakler, who served as Miss USA in 1995, resigned from the organization Wednesday. She decided she couldn't work for the pageant any longer after attending Trump's press conference Tuesday.
"I cannot with a clear conscience move forward supporting and promoting the Miss Universe Organization when I no longer believe in it or the contracts I signed committing myself as a youth," Moakler said in a statement issued by her publicist. "I want to be a role model for young women with high hopes of pageantry, but now feel it more important to be a role model for my children."
Trump took a much different tone Wednesday on "Good Morning America," saying the controversy surrounding Prejean was a boon.
"To a large extent, because of the great beauty of Carrie, it stirred a national debate on an issue that's been out there for a long time," he said.
But it was a set of topless photos, not Prejean's marriage views, that threatened her crown a month after she was named runner-up in the Trump-owned Miss USA pageant. During a news conference Tuesday, Trump announced that Prejean would not be stripped of her Miss California title or crown.
Trump today reiterated his approval of the pictures, telling "Good Morning America" that he knows the difference between good and bad photos.
"I reviewed the pictures. We're living in the 21st century," he said. "The pictures were fine. It was not a big deal."
Prejean, who turns 22 today, told "Good Morning America" that she isn't aware of any more racy photos that could be leaked but added that because she's been on so many photo shoots there's no way to be sure.
"If a photographer wants to release these photos just to make me look bad, then so be it," she said.
Prejean said she didn't consider the photos to be "semi-nude" and added that while she had been pressured to do so, she had never posed nude or semi-nude and always requested that her breasts be covered, and that she be photographed in full bottoms.
The racy photos, however "lovely" Trump believes they are, have drawn criticism from the many of the same conservative groups that initially backed Prejean for her gay marriage stance.
Trump said that admitting contestants who had done some modeling into the pageant and asking them tough questions had kept Miss USA relevant while the competing Miss America pageant has been taken off network television.
"Miss America's gonzo, and we're doing phenomenally," he said.
Prejean said she now wants to focus on her duties as Miss California and step out of participating in political debate.
She did, however, defend her association with the conservative National Organization for Marriage, saying it's an organization of respect, something she hasn't always gotten from her opponents.
During Tuesday's press conference, without mentioning his name, Prejean lashed out at Perez Hilton, the openly gay celebrity blogger and Miss USA pageant judge who asked what she thought of same sex marriage.