Last week, James Ammons had submitted a resignation letter stating his resignation would not take effect until Oct. 11. However, he waived a provision allowing him to give 90 days notice to the FAMU board in exchange for getting paid bonuses.
The school's governing board - which was holding an emergency meeting to discuss Ammon' resignation - voted to name current FAMU Provost Larry Robinson as interim president. Robinson had previously served in the administration of President Barack Obama as assistant secretary of commerce for oceans and atmosphere at the National Oceanic and Atmospheric Administration.
But trustees of the board also agreed to discuss Robinson's status as interim president again in August. Questions remain about whether other candidates should be considered - and whether an interim president is eligible to apply for the permanent job of president.
Ammons had vowed a month ago to remain at his job, despite a no-confidence vote from trustees in June.
During Monday's conference call, Ammons agreed to step down immediately but did not comment further about his decision.
The fallout began with the hazing death of drum major Robert Champion on Nov. 19. Champion's death put a spotlight on the hazing culture at the university, specifically within the famed Marching 100 band.
Trustees have complained about a lack of oversight of the band as well as lax management on other issues at the university.
Eleven FAMU band members face felony hazing charges, while two others face misdemeanor counts for alleged roles in Champion's hazing. They have pleaded not guilty.
Ammons was first brought on to help stabilize the school's financial troubles and threats to its accreditation. He first announced his plans to resign last week, the same day Champion's parents sued the university.