Destiny Velez tweeted filmmaker Michael Moore last week after he launched a campaign that encouraged people to make signs saying "We are all Muslim" and post photographs of themselves holding the signs online.
Her Twitter page has since been taken down, and Velez has apologized.
CNN obtained a screen grab of the page, and among the messages she originally sent were: "Muslims use our constitution to terrorize USA & plant gas stations," "there's NO comparison between Jews, Christians & Muslims. Jews nor Christians have terrorizing agendas in their sacred books, and "all what Muslims have done is provided oil & terrorize this country & many others!!!!!!."
The Miss Puerto Rico Organization issued a statement over the weekend distancing itself from her comments.
"In regards to Miss Puerto Rico, Destiny Velez's, recent actions and conduct; the Miss Puerto Rico Organization feels that her words do not represent the integrity and esteem of our program, nor that of our board members, our sponsors and partners, or the National Organization," it read.
"Miss Velez's actions were in contradiction to the organization, and therefore as a consequence of her actions, she has been suspended indefinitely. The Miss Puerto Rico Organization will not tolerate any actions or behavior contrary to the Miss Puerto Rico Organization."
The organization's statement also included an apology from Velez.
"I apologize to the people I have offended with my words. I am first and foremost an #UpStander and as such I stand up against bullying. The last thing I wanted to do was to bully anyone. Again, I apologize to anyone who felt offended with my words," she said.
Velez competed in this year's Miss America contest.
The Miss America Organization similarly tried to distance itself from her comments, releasing a statement saying it does not agree, condone or support what she said. MOA also said that it was working with the Miss Puerto Rico Organization to "resolve the issue."
Last week, Moore posted a picture of himself holding a sign reading "We are all Muslim" in front of Trump Tower in New York City. He was taking aim at Republican presidential candidate Donald Trump, who has called for a ban on all Muslims entering the United States.