By Dan Gilgoff, CNN.com Religion Editor

(CNN) - Conservative writer and activist Dinesh D’Souza, who attracted wide attention with his recent anti-Obama film “2016: Obama’s America,” resigned Thursday as president of a Christian college in New York after questions were raised about his marriage.

D’Souza had led The King’s College, a small but prestigious evangelical school in Manhattan, for the past two years.

His departure appeared to be set in motion by an article on the website of the evangelical magazine World that accused D’Souza, who is married, of sharing a hotel room with a woman whom he allegedly referred to as his “fiancé” at a Christian conference.

D’Souza has denied the allegations in the article, published Tuesday, and said he has been separated from his wife for two years and is in the process of getting a divorce.

“I am grateful for the past two years that I have spent as president of The King’s College. But now it is time to move on,” D’Souza said in a statement Thursday. “My resignation will enable The King’s College to go forward without distraction.

“And it will also enable me to address personal matters in my life as well as to pursue new opportunities made possible by success of my recent book and film,” said the statement, which was posted on his personal website.

D’Souza issued an in-depth rebuttal of the World article on the Fox News website on Wednesday. He did not immediately respond to requests for comment on Thursday.

“I met Denise three months ago,” D’Souza wrote in his rebuttal, referring to the woman mentioned in the World article. “We are not and have not been having an affair. Nor did we share a hotel room in Charlotte."

On Thursday, The King’s College board issued a statement about accepting D’Souza’s resignation.

“After careful consultation with the Board and with Dinesh, we have accepted his resignation to allow him to attend to his personal and family needs,” the college said in a letter to alumni.

“We thank him for his service and significant contribution to the College over the last two years."

The D’Souza flap has pitted two high-profile evangelical institutions – The King’s College and World magazine – against each other

King’s prides itself on being a new intellectual and urban face of evangelicalism, training Christians for careers in media, government and business and regularly attracting high-profile speakers like Mike Huckabee and the conservative editor Adam Bellow.

World is an intellectual bastion of American evangelicalism, edited by former George W. Bush adviser Marvin Olasky, who is also the former provost at The King’s College.

In his rebuttal, D’Souza said Olasky “vehemently opposed” his appointment as president at King’s and was using World magazine to “continue his vendetta.”

“Ultimately this is not just about Olasky or even World magazine,” D’Souza wrote. “It is also about how we Christians are supposed to behave with one another. And the secular world is watching.

“If my conduct was improper, wouldn’t it be the decent and charitable thing to approach me about it?” he continued. “Instead, here is a clear attempt to destroy my career and my ministry.”

Olasky did not immediately respond to a request for comment on Thursday. World magazine said on its website that its board of directors inserted prayers for King's and for D'Souza into the minutes of its meeting on Thursday.

"All-too-frequent reports of the sinful failing of our accomplished leaders bring us no joy," the prayer said, in part. "Instead, the searching light of your Holy Word illumines our hearts and minds to our own flaws and failures."