"This is unexpected, this is unanticipated," said Rufus Montgomery, a FAMU board member who had expressed doubts about Ammons' job performance.
Meanwhile, the famed Marching 100 band remains suspended for the coming year. And the university is dealing with a deficit in its athletic program, which has traditionally relied on the band to help draw large crowds to football games.
In October, 11 students will head to trial on charges related to the death of Robert Champion. The 26-year-old was fatally beaten by fellow band members during a hazing ritual aboard a bus parked outside an Orlando hotel following a football game against the school's archrival.
Montgomery and other trustees agreed late Wednesday to hold the emergency meeting to discuss finding a replacement for Ammons and the specific terms of his resignation. Even though Ammons' contract allows him to stay on the job 90 days, some board members said they still want to discuss how active a role he will play at the school.
Ammons, in a letter to the chairman of the university's governing board, said he plans to exercise a provision in his contract that allows him to remain at the school as a member of the faculty.
An alumnus and former top administrator of the school, Ammons was first hired five years ago to help steady FAMU in the wake of financial woes and threats to its accreditation.
But Champion's death on Nov. 19 put a spotlight on a hazing culture that he and other top FAMU officials had been unable to eradicate.
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.
Hazing that involves bodily harm is a third-degree felony in Florida.
Ammons did not explain why he chose Oct. 11 as his final day, or why he chose to announce his resignation Wednesday, the same day Champion's parents, Robert and Pamela Champion of Decatur, Ga., sued the university.
In his resignation letter, Ammons said his decision came after "considerable thought, introspection and conversations with my family."
He acknowledged "new challenges that must be met head on" at the university, but his letter did not mention Champion directly.
Still, the Champions applauded the move.
"Before the school can move forward, they have to do house cleaning," said Pamela Champion. "That means taking care of the entities that are there in order to prevent something like this from happening again."
FAMU math professor Calvin Robinson called Ammons' resignation "the worst news I've heard."
"I'm a second-generation Rattler," he said, referring to the nickname given to school alumni and students. "This is like the darkest day. ... Ever since Nov. 19 I saw this pressure coming, but I was hoping they'd realize the better strength of this man."
Given the intense pressure Ammons had been under, his move was not completely unexpected.
Florida Gov. Rick Scott at one point had recommended that Ammons be suspended from the job while investigations of Champion's hazing death were under way, a move that brought a nighttime protest outside the governor's mansion from hundreds of FAMU students.
The school's trustees gave Ammons a vote of no-confidence in June, after questioning his leadership in several areas, including what some saw as his lax attitude toward hazing and management of the band prior to Champion's death.
"This is not about hazing, this is about leadership, this is about serious lack of leadership," Montgomery said Wednesday.
Champion had bruises on his chest, arms, shoulder and back and died of internal bleeding. Witnesses told emergency dispatchers the drum major was vomiting before he was found unresponsive aboard the bus.
Ammons suspended the band right after Champion's death. He announced in May that the suspension would stay in effect for at least one more school year as officials moved ahead with trying to eliminate the hazing culture that surrounded the band. The president also recommended new stringent eligibility requirements for membership in the band.
Veteran band director Julian White was fired last year, but then his dismissal was placed on hold while the criminal investigation unfolded. He insisted he did nothing wrong and fought for months to get reinstated. He changed his mind in May and decided to retire after it was revealed that at least 100 band members were not students when Champion died.
Hours before Ammons' announcement Wednesday, Champion's parents added the university to a lawsuit they had brought against the bus driver, whom they alleged stood guard outside the bus while the hazing took place. The bus company owner initially said the driver was helping other band members with their equipment when the hazing took place.
The Champions claim Florida A&M University officials did not take action to stop hazing even though a school dean proposed suspending the band because of hazing concerns three days before their son died.
School officials also allowed nonstudents to play in the band, fell short in enforcing anti-hazing policies and did not keep a close eye on band members to prevent hazing, the lawsuit said.
The lawsuit seeks damages greater than $15,000, but does not give a specific amount. The university said in a statement that it knew the lawsuit was coming but had no further comment.