With billions in the balance, the battle may just be starting between the US government and universities.
www.bbc.com
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"No government - regardless of which party is in power - should dictate what private universities can teach," Harvard's president Alan Garber said in a letter posted on the university's website.
Not long after Harvard refused to agree to the White House's sweeping list of demands - which included directions on how to govern, hire and teach - the Trump administration froze $2.2bn (£1.7bn) of federal funds to the institution.
Many students and alumni lauded the university's decision to stand its ground, despite the consequences. Former President Barack Obama, an alumnus himself, called Trump's move "ham-handed" and praised Harvard as "an example for other higher-ed institutions".
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Trump's attacks on Harvard are not isolated - the government's antisemitism task force has identified at least 60 universities for review.
Nor did the latest move come out of the blue. Trump and his Vice-President JD Vance have long railed against higher education institutions. In 2021, Vance gave a speech that described universities as the "enemy".
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Harvard student Sa'maia Evans, who is an activist and member of the university's African and African American Resistance Organization, said the university's decision to take a stand was a long time coming.
"Harvard will only do that of which it is held accountable to," she told the BBC. She pointed to campus protests in the past few weeks - and the widespread criticism of Columbia's agreement with the Trump administration - as helping to put pressure on university officials.
"They know the public - they would experience public backlash" if they capitulated, Ms Evans said.
"It would be atypical (for) Harvard to do anything outside of what would be in its own interest."
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In his latest comments on the university, early on Wednesday, Trump attacked the "radical left" Harvard leadership and said the institution could "no longer be considered even a decent place of learning".
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"There's more the government can do if it wants to attack Harvard, and I'm not optimistic that it's going to stop after cutting $2.2 billion," Matthew Tobin, the academic representative on Harvard's student council.
Mr Tobin said the idea that the Trump administration was making these demands to help Harvard is "malarkey".
"It’s a total bad-faith attack," he told the BBC. "The funding cuts have to do with Trump attacking an institution that he views as liberal, and wanting to exercise more control over what people teach and how students learn and think."
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