The possible mismanagement of the school's finances and the subsequent reactions of students, faculty, alumni and organized protest groups attracted widespread media attention.

It has been reported that the Cooper Union financial crisis was due to a combination of problems caused by poor fiscal decisions, lack of accountability, the economic recession of the late 2000s, the selling off of the institution's assets, and taking on significant debt due to the 2009 building of 41 Cooper Square, which cost the school US$175 million.

The New York State Attorney General reached an agreement in September 2015 to settle a lawsuit filed by the Committee to Save Cooper Union against the board of trustees.

A consent decree, signed by the attorney general and both parties in the lawsuit and pending court approval, outlined additional fiscal and administrative oversight of the school by the attorney general and made provisions for students, alumni, and faculty, who would work with the board of trustees to determine how Cooper Union could return to a tuition-free school.

[60] In December 2015, Acting President Bill Mea noted "I have projected numbers out to fiscal 2019 and 2020, and I think it can become financially sustainable by those periods and thereafter", with tuition.

[64][65] Friends of Cooper Union (FOCU), composed of alumni, students, faculty, and staff, met in December 2011 to generate its own solutions to the financial crisis.

[66] Committee to Save Cooper Union, Inc. (CSCU), a voluntary association of faculty, students, and alumni, formed on December 16, 2013, in order to investigate and remedy serious issues regarding the fiscal and academic management of the school.