Much like public institutions and for-profit companies, nonprofits find themselves under the Trump administration’s ideological microscope. Amid ongoing court battles weighing the legality of White House directives around federal funding, many nonprofits are stuck in a state of limbo, unsure whether they will be forced to cut programs and staff, or change their core function in order to survive the president’s purge of bankrolling organizations that don’t align with his agenda.

Organizations whose work centers around diversity, equity, and inclusion initiatives, assisting undocumented immigrants, serving LGBTQ communities, and fighting climate change worry their missions could be in direct conflict with executive orders . A Feb. 6 White House memo to agency heads directed them to review current funding to nongovernmental organizations and align future funding decisions with “the goals and priorities” of the Trump administration.

That’s in addition to Department of Government Efficiency cuts to certain federal agencies, which have had downstream effects on funding previously pledged to nonprofits. Elon Musk, the head of DOGE, wrote in a recent post on X that “Government-funded NGOs (a contradiction in terms) are probably the biggest source of fraud.”

Nonprofit experts and leaders told the Globe that the Trump administration is straining the traditional relationship between nonprofits and the federal government, which has defined how public services reach communities across the country for decades.

“In a lot of other countries, the role that we rely on nonprofit organizations to do is often done by government provision more directly,” said Claire Dunning, an associate professor at the University of Maryland’s School of Public Policy. The administration’s recent decisions, she said, are “bringing to light what many people have quietly known, which is that the nonprofit sector relies quite heavily on government money. The notion that it is a separate sector has truth to it, but the boundaries between government and nonprofits are quite porous.”

The White House did not return a request for comment.

That relationship really started to coalesce in the 1960s, Dunning said, when Lyndon B. Johnson launched his Great Society programs and contracted nonprofit organizations to provide social services that the government previously brought directly to citizens. It was a way for the federal government “to appear responsive on the ground, but to maintain degrees of control” over decision-making, Dunning said.

Jim Klocke, CEO of the Massachusetts Nonprofit Network , said this symbiotic relationship has reached “a whole new level of uncertainty and turbulence. If it only affected the people who were moving the funds that would be one thing, but this turbulence has real effects on real people at the end of the day.”

Those interviewed for this story warned that nonprofits are embedded in every facet of American life and, when they lose federal funding, everyone feels the consequences. That is especially true, they said, for the country’s most vulnerable populations — like low-income communities, immigrants, and people experiencing homelessness or food insecurity — who rely upon social services.

Food banks across New England, for example, are scrambling to meet the needs of the hungry after the Trump administration last month cut $1 billion in Department of Agriculture funding.

“It’s going to be a very painful civics lesson in making visible what has been deeply invisible,” Dunning said.

In 2023, the average nonprofit generated 25 percent of its revenue from government sources, according to the Urban Institute, a left-leaning think tank that conducts economic and social policy research.

Nationally, “there is not enough money in all of philanthropy combined to do what the federal government is able to do with its resources,” said Jeff Moore, chief strategy officer at Independent Sector , an organization that specializes in nonprofit-related public policy. Charities received more than $267 billion in government grants in 2021 , according to the Urban Institute, almost three times the amount given by foundations.

Even so, the ideological strings attached to government funds under Trump have led one nonprofit to swear off future federal financial assistance altogether.

826 Boston, a writing, tutoring, and publishing organization that works with K-12 students, announced in early April that it would withdraw from receiving future federal funding . Corey Yarbrough, the organization’s executive director, said the decision was made for fear that the Trump administration’s DEI restrictions would limit what students in their programs could write about.

“The preservation of our democracy is based on free speech and being able to articulate your perspective without fear of harm or retaliation,” Yarbrough said. “It’s a very scary time and I’m very concerned about the erasure of underserved and historically oppressed communities.”

But the choice wasn’t pain free. Yarbrough said 826 Boston receives about $250,000 a year — or 9 percent of its annual budget — from the federal government by way of AmeriCorps.

“It was a very difficult decision, but I ultimately must say I feel like we are in a privileged place to be able to stand on our integrity,” Yarbrough said, adding that he hopes foundations, corporations, private donors, and local government will help fill the funding gap.

However, Klocke warns that “the health of the economy and the health of the nonprofit sector are really pretty tightly connected to each other.” Given the state of the stock market following Trump’s tariffs, Klocke said, it wouldn’t be surprising to see both businesses and individuals scale back their charitable donations.

Dean, of the Tennessee Nonprofit Network, said he’s already seen some nonprofit donors become skittish about the potential political backlash to their charitable contributions.

“They don’t want their names on a donor lists because they’re scared that’s going to be subpoenaed,” he said. “Foundations are saying, ‘We’re going to give you this money, but don’t post on your Facebook, don’t put us in your annual report, put us in as anonymous.’”

A retreat in both public and private giving to nonprofits could hold serious consequences for the health of the American labor market. Nonprofits employ 12.7 million people , or about 10 percent of the country’s private-sector employees, according to the Urban Institute.

Still, Moore said, nonprofits must remain pragmatic.

“We try really hard here not to be operating in the doomsday scenario. We’re trying to be very smart and attentive to the potential without being naive,” he said, adding that the goal is to work with the Trump administration in good faith to serve the public. “We hope they take us up on that opportunity. We’re doing everything we can to put the open hand forward, but also to be smart about the times we’re operating in.”

It’s a moment that Hal Cato, CEO of the Middle Tennessee Community Foundation , described as “uncharted waters.”

But that’s exactly why, he said, in the nonprofit world, “this is not the time for egos to get in the way of how we can work together across missions and across a somewhat competitive funding landscape to support one another.”

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