JACS Charge Against Columbia: 2025 Settlement and Compliance Terms

Columbia University’s federal funding settlement with the Trump administration, reached on July 23, 2025, requires the university to pay $200 million over three years plus an additional $21 million to the Equal Employment Opportunity Commission, in exchange for restoration of roughly $400 million in frozen research grants and renewed eligibility for federal funding. A separate and much earlier matter, a $9.5 million civil fraud settlement in 2016, resolved claims that Columbia had overbilled the National Institutes of Health on hundreds of research grants. The two cases involve different allegations, different agencies, and different legal theories, but together they define Columbia’s recent history with federal grant money.¹²

What the 2025 Settlement Covers

The Trump administration froze approximately $400 million in federal grants to Columbia in early 2025 and placed most of the university’s $1.3 billion in annual federal funding on hold. The freeze followed investigations into alleged violations of Title VI of the Civil Rights Act over Columbia’s handling of antisemitism on campus after the October 7, 2023, Hamas attacks.¹

Under the July 23, 2025, agreement, Columbia agreed to pay $200 million to the federal government over three years and $21 million to settle EEOC workplace harassment investigations. More than $20 million of the settlement was directed to civil rights violations against Jewish employees, which the White House described as the largest such settlement for victims of antisemitism.³⁴

Columbia made no admission of wrongdoing and specifically denied liability on the Title VI allegations. Acting President Claire Shipman said the agreement preserved academic independence. Todd Wolfson, president of the American Association of University Professors, called the deal a “devastating blow to academic freedom and freedom of speech at Columbia.”³

What Columbia Agreed to Change

The settlement attached detailed compliance conditions to the restored funding. Columbia agreed to adopt the International Holocaust Remembrance Alliance definition of antisemitism, appoint new faculty to joint positions in the Institute for Israel and Jewish Studies, name coordinators to handle antisemitism allegations, and roll out university-wide training. The university also agreed to end programs promoting “race-based outcomes, quotas, diversity targets, or similar efforts” and to keep admissions and hiring merit-based.⁴

On protests and security, the agreement required strict enforcement against disruptive protests, banned masked protests, mandated trained security officers, and formalized cooperation with the New York Police Department. Student disciplinary authority moved from the faculty senate to the Office of the Provost, and the University Judicial Board was restructured to include only faculty and staff, with students removed.⁴⁵

Columbia also agreed to review its Middle Eastern regional programs, appoint new faculty to promote “intellectual diversity,” add application questions asking international students why they want to study in the United States, and share admissions data with the federal government for auditing. The agreement explicitly states that “no provision of this agreement, individually or taken together, shall be construed as giving the United States authority to dictate faculty hiring, university hiring, admissions decisions, or the content of academic speech.”⁶

Oversight and Compliance Reporting

An independent resolution monitor oversees compliance with the agreement. The initial monitor, Bart Schwartz of Guidepost Solutions, was replaced in January 2026 by Charles J. Cooper, founding partner of the Washington, D.C. firm Cooper & Kirk, after difficulties arose with the original monitor’s billing structure. Cooper previously served as assistant attorney general under President Reagan and argued before the Supreme Court in defense of California’s ban on same-sex marriage.⁷

Columbia’s first semi-annual compliance report, dated April 1, 2026, tracked progress on 24 agreement items. Eighteen were marked “complete” or “satisfied to date,” and five remained “in progress,” including reviews of Middle Eastern studies programs and admissions data auditing. The university reported paying a $66.67 million installment toward the $200 million settlement and funding the $21 million EEOC claims fund. Columbia also prohibited diversity statements in academic job postings and began requiring student attestations of commitment to civil discourse, effective by fall 2026.⁵

The Earlier 2016 Grant Billing Settlement

Nearly a decade before the Title VI dispute, Columbia settled a separate federal matter involving research grant billing. In July 2016, the university agreed to pay $9.5 million to resolve a civil fraud lawsuit alleging that between July 2003 and June 2015, Columbia applied its higher “on-campus” indirect cost rate of approximately 61% to 423 NIH grants, even though the research was primarily performed at facilities owned and operated by New York State and New York City. The correct off-campus rate was either 26% or 29.4%.²

Columbia admitted that it had applied the on-campus rate to those grants despite the research taking place in space it did not own or operate, and that it had submitted certified reports to the NIH using the higher rate. The government joined a private whistleblower lawsuit filed under seal under the False Claims Act, and U.S. District Judge Paul A. Engelmayer in the Southern District of New York approved the settlement.²

The Indirect Cost Rate Dispute

The same category of charge at the heart of the 2016 case, indirect cost recovery, became a separate flashpoint in 2025. Columbia’s federally negotiated indirect cost rate for on-campus research stood at 64.5% as of 2024. In fiscal year 2024, Columbia received $348.9 million in indirect cost recoveries, representing 26.3% of its $1.3 billion in total federal research grants.⁸⁹

In February 2025, the NIH announced it would cap indirect cost payments at a flat 15% for all grants accepted after February 10, 2025, down from individually negotiated rates that typically ranged from 30% to 70% at major research universities. The Association of American Medical Colleges estimated the cap would have cost the research enterprise $6.5 billion in previously committed funding.¹⁰

Three lawsuits challenged the cap, brought by coalitions that included state attorneys general, the Association of American Medical Colleges, the American Council on Education, and individual universities. In April 2025, U.S. District Judge Angel Kelley issued a permanent injunction blocking the cap, and on January 5, 2026, a unanimous panel of the U.S. Court of Appeals for the First Circuit affirmed. The court found that the NIH had violated its own regulations and a congressional appropriations provision prohibiting unilateral changes to indirect cost reimbursement.¹¹¹²

Similar caps attempted at the National Science Foundation, the Department of Energy, and the Department of Defense were struck down or blocked in 2025. The Trump administration let the deadline to appeal the NIH ruling to the Supreme Court pass in April 2026, effectively ending the litigation.¹³ In August 2025, President Trump signed an executive order directing federal agencies to prioritize institutions with lower indirect cost rates when making funding decisions.¹⁰

Operational Fallout and What Remains Uncertain

The funding freeze had tangible consequences before the July 2025 settlement restored most grants. Columbia laid off nearly 180 researchers and froze hiring at the Vagelos College of Physicians and Surgeons. As of August 2025, Columbia’s School of Public Health and medical center remained in “austerity mode,” with hiring delays and reduced slots for Ph.D. students.¹⁴¹⁵

After the settlement, Columbia reported that “almost 99 percent” of canceled federal grants were restored and the university regained eligibility to apply for new federal research funding. A subset of grants in research areas “out of favor with the White House,” such as transgender health, remained unfunded as of August 2025.¹⁴

Even with the settlement in place, Columbia faces continued uncertainty. A Trump administration budget proposal released in April 2026 called for cutting more than $15 billion from federal science agencies in fiscal year 2027, including a 54.7% reduction to the National Science Foundation and a 13% cut to the NIH. Federal grants accounted for 19% of Columbia’s operating budget in 2025, and Congress was expected to vote on those appropriations in September 2026.¹⁵

1
Columbia University Office of the President. Resolution of Federal Investigations and Restoration of the University’s Research Funding
2
U.S. Department of Justice. Manhattan U.S. Attorney Announces $9.5 Million Settlement With Columbia University
3
NPR. Columbia Trump Administration Settlement Details
4
The White House. Fact Sheet: President Donald J. Trump Secures Major Settlement With Columbia University
5
Columbia Spectator. In First Report on Active Compliance With Trump Deal, Columbia Mandates Civil Discourse Attestation
6
Columbia University. Federal Resolution Agreement
7
Columbia Spectator. Lawyer Who Argued for State Ban on Same-Sex Marriage Named New Independent Monitor
8
Columbia University Finance. Facilities and Administrative Costs
9
Columbia Spectator. Shipman to Discuss Caps on Research Indirect Costs on Capitol Hill
10
Chemical & Engineering News. NIH Research Funding Indirect Cost Cap Lawsuit
11
American Council on Education. Association Lawsuit NIH F&A
12
Science. Appeals Court Agrees NIH Cannot Reduce Overhead Payments to Academic Institutions
13
STAT News. Trump Administration Drops NIH Indirect Costs Court Challenge
14
The New York Times. Columbia Trump Federal Money Returned
15
Columbia Spectator. Columbia Stands to Lose Tens of Millions as White House Reopens Push to Cut Science Funding