The Trump administration is rapidly expanding a campaign of retaliation and intimidation against nonprofits across the United States, with threats ranging from the revocation of tax-exempt status to the embedding of government agents in independent organizations. Harvard University is now at the center of what critics say is a broader effort to dismantle civil society, as the administration threatens to strip the Ivy League institution of its 501(c)(3) status following its refusal to comply with political demands.
CNN first reported that the Internal Revenue Service, now led by an interim commissioner aligned with President Donald Trump, is weighing whether to revoke Harvard’s tax exemption. The move came shortly after Trump wrote on Truth Social, “Perhaps Harvard should lose its Tax Exempt Status and be Taxed as a Political Entity if it keeps pushing political, ideological, and terrorist inspired/supporting ‘Sickness?’”
The president’s threat followed Harvard’s rejection of several administration demands, including a call to derecognize pro-Palestine student groups, audit academic programs for viewpoint diversity, and expel students involved in a 2023 protest on the Harvard Business School campus. Harvard President Alan Garber responded publicly, saying, “No government—regardless of which party is in power—should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue.”
The administration also froze over $2 billion in federal funding to Harvard after its refusal to comply. In a statement, Harvard warned that such an “unprecedented action” would “endanger our ability to carry out our educational mission.” The university added, “It would result in diminished financial aid for students, abandonment of critical medical research programs, and lost opportunities for innovation. The unlawful use of this instrument more broadly would have grave consequences for the future of higher education in America.”
The legal and constitutional implications are drawing alarm from lawmakers and civil liberties experts. Senator Ron Wyden (D-Ore.), chair of the Senate Finance Committee, said, “The First Amendment and federal tax law make clear no president can raise a university’s taxes because he doesn’t like what they teach.” He warned, “If this corrupt shakedown scheme stands, nonprofits from churches to temples to hospitals could be forced to echo Trump’s MAGA line or see their taxes hiked. Any Republican who claims to believe in the Constitution and doesn’t speak up is responsible for what happens next.”
Representative Jerry Nadler (D-N.Y.) called the threat “bullshit” and said, “This deeply disturbing and blatantly unlawful action is Trump’s latest foray in his war to politicize higher education and degrade any institution that refuses to bend the knee.”
Harvard is not alone. The administration’s attack on nonprofit independence is expanding through an agency known as the Department of Government Efficiency (DOGE), led by Tesla and SpaceX CEO Elon Musk. The Vera Institute of Justice, a nonprofit focused on criminal justice reform, revealed that DOGE attempted to embed federal agents within its operations, citing its past receipt of federal grants. Though the group’s legal team successfully pushed back—after noting its grants had been terminated—DOGE reportedly informed Vera that its plan was part of a broader strategy to “assign DOGE teams to every institute or agency that has congressional monies appropriated to it.”
Vera president Nick Turner said, “We are sharing this information broadly with other nonprofits that receive federal funding—so they can be aware of DOGE’s plan to assign teams to investigate their operations.” Turner called it “this latest intimidation tactic targeting private, independent mission-driven organizations and undermining civil society.”
The National Council of Nonprofits echoed the concern. “The attempted intrusion by DOGE—a temporary, un-elected and non-Congressionally approved agency—toward the Vera Institute should alarm every American,” said its president Diane Yentel. “This action by DOGE sets a dangerous precedent, leaving any recipient of federal funding—nonprofit, for-profit, and individuals alike—vulnerable to the whims of this destructive group. DOGE and The Trump Administration’s professed commitment to free speech and financial efficiency falls flat when their actions selectively target and weaken groups whose missions they may oppose.”
DOGE officials reportedly cited their federal takeover of the U.S. Institute of Peace (USIP)—a nonprofit created by Congress—as a success story. In that case, DOGE fired the board and leadership and transferred control of the institute’s headquarters to the federal government.
The scope of DOGE’s effort is vast. The Urban Institute found that over 103,000 nonprofits received $267 billion in government grants in 2021. Advocacy groups say this enormous intersection between nonprofits and public funding is now being weaponized by the Trump administration to impose political control over independent organizations.
Elon Musk has reinforced the administration’s stance on social media. Last month, he wrote, “The Democrat government-funded NGO scam might be the biggest theft of taxpayer money ever.” Musk has also repeatedly accused climate and civil rights nonprofits of fraud and called for prosecutions without evidence.
Climate organizations and environmental groups now fear they are next. Several groups are preparing for what they believe could be a targeted executive action against them on Earth Day. “There’s lots of rumors about what terrible thing [Trump] wants to do on Earth Day, to just give everybody the middle finger,” said Brett Hartl of the Center for Biological Diversity. Bloomberg Law reported that legal teams at environmental organizations are preparing for possible revocation of tax-exempt status or funding seizures. In some cases, sources said, groups fear being labeled as “domestic terrorists.”
Kieran Suckling, executive director for the Center for Biological Diversity, said his organization would take legal action if attacked. Bill McKibben, environmentalist and founder of 350.org, said, “It was perhaps inevitable that Trump and his team would target us; together we’ve been making life harder for his clients in the fossil fuel industry. And in the new America, if you don’t knuckle under you get a knuckle sandwich. Figuratively speaking. One hopes.”
Harvard cyberlaw instructor Alejandra Caraballo has also been outspoken about the implications of this campaign. “The end goal is to destroy all of civil society. NGOs include everything from community clinics to civil rights orgs. It means the end of the ACLU, NAACP, and all advocacy orgs,” she wrote. “Fascists need to crush civil society orgs because they are a bulwark of liberalism. They democratize access to power and institutions while defending civil liberties. That’s what all of this is about.”
Rep. Lloyd Doggett (D-Texas), who previously led efforts to block Republican legislation that would expand presidential power to revoke nonprofit status, warned, “The threat to nonprofits is re-emerging as Trump targets Harvard for standing for academic freedom against his war on higher education and intellectual inquiry.”
Cole Leiter, executive director of Americans Against Government Censorship, warned that the threats to Harvard and groups like Vera are only the beginning. “Today the organization being threatened by the government is Harvard, tomorrow it could be a community organization feeding the hungry or helping children with disabilities,” Leiter said. “If the Trump administration decides it wants to target schools, groups, churches, or welfare organizations because they don’t fall in line with their political agenda, it will open the door for any future administration to use this same unchecked power against more American citizens.”
“This is a dangerous practice,” he added, “and it is one that should end before it ever begins.”
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