Liberty University has accepted the resignation of President and Chancellor Jerry Falwell Jr after he and his wife became embroiled in sex scandal allegations.

Giancarlo Granda, 29, said he had an affair with Becki Falwell that started eight years ago.  He claimed that she approached him when he was working as a pool boy at the Fontainebleau Hotel in Miami in March 2012. 

Explosively, he claimed that Jerry liked to watch the pair during their sexual liasons. 

Jerry denied the allegations. 

"Becki had an inappropriate personal relationship with this person, something in which I was not involved — it was nonetheless very upsetting to learn about," Falwell said in a statement to the Washington Examiner.

Becki has admitted to the affair but refuted Granda's claims that her husband watched. 

In a statement on Tuesday, Liberty U trustees said they had accepted Jerry's resignation "effective immediately". 

"After agreeing yesterday to immediately resign then reversing course, Falwell, through an attorney, sent the resignation letter late last night to members of the Board's Executive Committee pursuant to the terms of his contract of employment," the board said.

"The Executive Committee met this morning and voted to accept all the resignations immediately and recommend ratification to the full Board. Later this morning, the full Board gathered via conference call and unanimously voted to affirm the decision of the Executive Committee.

"Falwell's severance compensation was dictated by the terms of his pre-existing employment agreement without any adjustment by the University or its Board."

Jerry had already been on indefinite leave from the university after an embarrassing controversy over a photo posted to his Instagram in which he had his pants unzipped, exposing his underwear and midrift. 

In comments to ABC News regarding his resignation, Jerry said: "I was never called to be a pastor, my calling was to use my legal and business expertise to make Liberty University the evangelical version of Notre Dame.

"Some of us are called to be preachers, that wasn't mine. I was called to make Liberty University the greatest Christian university in the world and I couldn't have done that as a preacher."

Acting Board Chairman Allen McFarland said board members had exemplified "the unity of Christ" in its handling of the scandal.

"Liberty University's future is very bright and in capable hands of leaders who are committed to being good stewards of what the Lord has entrusted," he said.