Reed was tearful during a 15-minute goodbye in front of players and parents.
"We've been around here trying to change things," Reed said. "My vision for change, probably moving too fast for a lot of people. I'm not withdrawing my name, as they said. They don't want me here. They do not want me here because I tell the truth."
Reed also tweeted an announcement that detailed, "After weeks of negotiations I've been informed that the University won't be ratifying my contract and won't make good on the agreement we had in principle, which had provisions and resources best needed to support the student athletes.
"I was committed to coaching and cultivating a relationship with the University, Players, Community and the Fans. It's extremely disappointing this won't be happening," Reed said.
On Dec. 27, Bethune-Cookman announced that the school and Reed had "entered an agreement in principle ... to be its 16th head football coach." Its previous coach, Terry Sims, was fired in late November after going 2-9 in back-to-back seasons.
The decision to not ratify Reed's contract comes after the Pro Football Hall of Famer caused a stir when he went on social media and complained that his office had not been cleaned before he arrived. Reed later apologized for the profanity-laced post and apologized for it again Saturday.
"I'm a good man, not perfect," he said. "We all make mistakes, and I apologized for mine."
Bethune-Cookman said in a statement on Saturday that it had "decided not to proceed with contract negotiations" with Reed.
"While we appreciate the initial interest in our football program displayed by Mr. Reed during the course of recent weeks, we are also mindful of the qualities and attributes that must be exhibited by our institutional personnel during what have been uniquely challenging times for our campus as we recover from the impact of two hurricanes during this past fall semester," the statement said in part.
Bethune-Cookman, a historically Black university in Daytona Beach, Florida, has won six MEAC championships since 2000 but has struggled after joining the SWAC in 2021.
The program was hoping to find the same success that Jackson State did when it hired Deion Sanders as coach. Now at Colorado, Coach Prime called Reed during his goodbye Saturday and offered help and guidance.
"I know you do not want to leave those kids," said Sanders, who was briefly teammates with Reed in Baltimore. "Sometimes in life, you got to walk away."
Reed, 44, has spent the past three seasons in a support-staff role at his alma mater, Miami, most recently as a senior football adviser under coach Mario Cristobal.
Information from The Associated Press was used in this report.