As she opened her remarks, some students stood and turned their backs to her. At times hecklers drowned out her remarks.
Perhaps foreseeing the resistance she'd face during her speech, DeVos told the crowd, "While we will undoubtedly disagree at times, I hope we can do so respectfully. Let's choose to hear one another out. I want to reaffirm this administration's commitment to and support for (historically black colleges and universities) and the students they serve."
DeVos managed to get through her remarks, wrapping up in about 20 minutes.
But another huge chorus of boos erupted when she was awarded an honorary doctorate, and again when she said she would visit the home of school founder Mary McLeod Bethune to pay her respects.
School president warns students
Early in her speech, DeVos told the crowd, "One of the hallmarks of higher education, and of democracy, is the ability to converse with and learn from those with whom we disagree."
At that point, the commencement became so rowdy that school President Edison Jackson interrupted DeVos' remarks to issue a warning to graduates.
"If this behavior continues, your degrees will be mailed to you," he said. "Choose which way you want to go."
Many of the standing graduates took their seats, but a few remained standing, prompting Jackson to implore them again to sit down.
The tone seemed to soften as DeVos continued, exhorting the students to embrace service as they enter the next phases of their lives.
"The human heart is hard-wired for service, and it's embedded in the DNA of this institution," she said.
During the speech, a sophomore, Bobbie Luke, his right fist aloft, was escorted out of the Ocean Center. He told CNN he didn't know why he was removed.
"I'm standing with my seniors, man. No one likes her, man. Period," he said. "I don't like what she said, and nothing at the end of the day is going to change my opinion."
DeVos 'understood the legacy behind my story'
Ca'Netta General was one of three students whose triumphs over hardships DeVos mentioned in her speech. General said she was honored that someone "would consider my story to be deemed worthy enough to be mentioned during graduation as a success story, not to give up."
General, 27, of West Palm Beach, Florida, enrolled at Bethune-Cookman at age 24. She credited her family and mentors who encouraged her and "kept me in their prayers." A mass communications graduate, she will attend Howard University and pursue a graduate degree in transformational leadership, she said.
"I know that she understood where I was coming from and she understood the legacy that was behind my story," General said of DeVos.
'Real pioneers' remark follows DeVos
Before DeVos' address, several students told CNN there was no place for her at commencement because of her comments in February about HBCUs, and they were miffed they didn't have more say in picking a graduation speaker.
Though DeVos quickly walked back those comments and conceded the schools were born of racism, it was not enough for many on this campus, nor those who hold it dear.
"She's the secretary of education. Your job is to do research. Your job is to be committed to academia and know exactly what you're talking about, ... what context you're saying it in," said 1996 graduate Fedrick Ingram, vice president of the Florida Education Association.
Asked if too much was made of DeVos' initial take on historically black campuses, he emphatically said no, calling her remark "blatant ignorance."
Peaceful protests against DeVos' appearance began last week at Bethune-Cookman, with demonstrators holding placards that read "DeVos No" and "Our tax $s pay for public education." The NAACP Florida State Conference has urged the university president and board chairman to step down.
"The students booing and some cheering is a reflection of their concern about the policies of the Department of Education," NAACP President Cornell Brooks said. "So let's be clear about this, the issue here is not the civility of the students but rather the policy of the secretary."
Brooks emphasized students were exercising "their First Amendment right to boo."
On Tuesday, Dominic Whitehead, a 2010 graduate, led a group that delivered what he said were about 60,000 signatures asking the university to stop her speech.
But only about 6,000 of the petitions were properly filled out, and of those, the majority came from outside the campus and Daytona Beach, said a university official who asked not to be named because he didn't want to steal the spotlight from the university's president.
DeVos' detractors charge that the education secretary has reduced consumer protections for student-loan repayment plans and amnesty programs, something many Bethune-Cookman students depend upon. They're also opposed to her previous negative remarks about public education, of which many Bethune-Cookman students are products.
President Donald Trump over the weekend issued a statement saying, "Secretary DeVos chose an HBCU as the venue for her first commencement address to demonstrate my administration's dedication to these great institutions of higher learning."
'They're both female'
Junior Jasmine Smith, who helped deliver petitions to university leaders, said she felt DeVos was an inappropriate choice for her school's spring commencement because there's so little common ground between her and the students she was to address.
"I believe (graduates) deserve a speaker who could relate to them as far as the struggle we go through within the education system, and I feel like she cannot relate in that aspect," Smith said.
Asked about a university news release that compared DeVos to the school's founder -- saying they both appreciated "the importance of opportunity and hope for students to receive an exceptional education experience" -- Smith smirked.
"Similar qualities -- they're both female, but that's pretty much all I can think of," she said.
Free speech under attack?
Students and graduates denied that their opposition to DeVos infringed on others' First Amendment rights. This isn't about the free exchange of ideas, they said.
"I'm all for building bridges, and I welcome Secretary DeVos to meet me and more undergraduate students ... but not at a commencement speech where it's so one-sided," Smith said.
Added Ingram, "If you want to have free speech, if you want to have a dialogue, if you want to learn, this is not the place for that. A commencement exercise is not a dialogue. It's a monologue, so she's going to have a one-way opportunity to talk about her ideology."
DeVos met with a group of students before her address, school officials said Wednesday. General said she was in that group.
Students asked DeVos questions, including about more funding for students who study abroad, General said.
"She seemed as if she was genuinely interested in us," she said. "It didn't seem like it was for publicity or for a couple likes on Twitter."
Jackson, the university president, defended the invitation, saying it benefits students to hear from those with controversial ideals and differing beliefs.
"If our students are robbed of the opportunity to experience and interact with views that may be different from their own, then they will be tremendously less equipped for the demands of democratic citizenship," he said in a statement.
Students and alumni reserved plenty of their angst for Jackson and other members of the school's leadership. They questioned why they didn't learn DeVos would be the speaker until final exams were already underway, giving them little time to respond.
Whitehead, the petition organizer, said the school's founder "would not be pleased with (DeVos) being the commencement speaker" and would have demanded that the nation's education chief have a real conversation with pupils -- about public education, charter schools and other issues -- before allowing her to address the student body.
"Dr. Bethune stood for education for all people," Whitehead said. "Before giving a message, I think you need to hear the message and hear what HBCUs are about and the issues that affect us."
In a statement after the commencement address, DeVos said she was grateful for the chance to give the speech, and "show my deep respect for the important legacy of Dr. Bethune."
"Her life's work was to help all students succeed, and it was clear today that she succeeded beyond comparison," DeVos said.
Correction: An earlier version of this story stated DeVos had been scheduled to speak for an hour or more. The commencement program did not say how long she was scheduled to speak.