[3] While serving as President of the University of Michigan, he was at the center of two notable United States Supreme Court cases regarding the use of affirmative action in admissions processes.

[12] In the Grutter case, the Court found by a 5–4 margin that the affirmative action policies of the University of Michigan Law School were constitutional.

But at the same time, it found by a 6–3 margin in the Gratz case that the undergraduate admissions policies of Michigan were not narrowly tailored to a compelling interest in diversity and 20 predetermined points are awarded to underrepresented minorities, and thus that they violated the Equal Protection Clause of the Fourteenth Amendment.

[17] Bollinger was the subject of criticism for his role in advocating the expansion of the university into the Manhattanville neighborhood and the use of eminent domain to help it seize property there.

Bollinger attempted to expand the international scope of the university, took frequent trips abroad and invited world leaders to its campus.

Bollinger was criticized for taking a neutral public position on controversies regarding the Middle East Languages and Cultures (MEALAC) department.

[19][20] In 2013, Bollinger's total compensation was $4.6 million, making him the highest paid private college president in the United States.

[21] At a January 2021 rally during a student tuition strike protesting the university's tuition rates, Young Democratic Socialists of America organizers cited as further evidence of alleged inequitable allocation of university resources the fact that Bollinger's salary had been frozen that year, while Barnard College administration's salaries had been cut, including by 20 percent in the case of Sian Beilock, Barnard College's president.

[26][27][28] Bollinger described the event as part of "Columbia's long-standing tradition of serving as a major forum for robust debate, especially on global issues.