It was a turning point in the Trump administration’s efforts to bring elite academia to heel. The White House had made an example of Columbia University by axing $400 million in federal grants, and now it was saying that the Ivy League school would have to acquiesce to a bill of demands if it were to have any hope of recouping the money.

One of the dictates handed down in March involved the university’s Middle Eastern, South Asian and African Studies Department. The White House, which said Columbia had failed to protect Jewish students from antisemitic harassment, wanted the school to strip the department of its autonomy, a rare administrative step that was viewed as a serious blow to academic freedom. The university, which was the first high-profile target in the administration’s war on higher education, had a different idea.

Quietly, university officials were trying to navigate a narrower path, appeasing President Trump by cracking down on protests and making changes to student discipline. But the measures adopted by Columbia were not as drastic as what the White House had wanted. The university’s leaders sought to shape Mr. Trump’s demands through negotiation instead of fighting them through litigation, and to do that while maintaining core ideals that had defined the university for nearly 275 years.

Columbia’s approach stood in stark contrast to the tack taken by Harvard University, which turned to the courts to fight Mr. Trump.

While many in the academic world have accused Columbia of caving to Mr. Trump’s pressure, the university’s strategy — so far — has limited the bleeding to $400 million, even as Harvard has absorbed cut after cut, stretching into billions of dollars. While opponents of the Trump administration’s crackdown have lauded Harvard for standing its ground, it is far from clear which school will be better off in the long run. And the question remains whether Columbia’s path can offer a road map for other universities attacked by the president.

“Following the law and attempting to resolve a complaint is not capitulation,” Claire Shipman, Columbia’s acting president, said last week in a statement. “We must maintain our autonomy and independent governance.”