World magazine reported Tuesday the conservative author and political commentator had attended a Christian conference last month and stayed in a hotel with Denise Odie Joseph II, even though he is married to his wife of 20 years, Dixie. D'Souza had introduced Joseph as his fiance, World reported.
The King's College board of trustees said in a statement it had accepted D'Souza's resignation "effective immediately," Christianity Today reported.
The board said in a news release D'Souza acknowledged his actions "have not been consistent with the standard of leadership required for the position of president at The King's College, and have created a distraction that would make it difficult, if not impossible, to continue in my role without adversely affecting the students and school I have grown to love."
A subsequent release left that quote out and said the board wanted to allow D'Souza "to attend to his personal and family needs," Christianity Today reported.
The story published Tuesday in World said D'Souza and Joseph shared a room at the Truth for a New Generation 2012 conference in Spartanburg, S.C., and when confronted by conference speaker Alex McFarland, D'Souza said "nothing happened."
In an interview with Christianity Today, D'Souza Wednesday rejected McFarland's account. He said he and his wife have been separated for two years with no prospect of reconciliation, and he began divorce proceedings in September.
D'Souza is best known as the writer, director and star of the documentary "2016: Obama's America," based on his 2010 book "The Roots of Obama's Rage."