Eight years ago, when a newly inaugurated President Trump cracked down on illegal immigration, many U.S. houses of worship became houses of refuge. Just days after his second swearing-in, the tide is turning.

A new Trump directive tossed out longstanding rules that restricted federal immigration authorities from making arrests at churches and other so-called sensitive locations such as schools and hospitals. It is part of a cascade of orders meant to accelerate the deportation of millions of immigrants living in the U.S. illegally.

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A sign prohibiting ICE and Homeland Security from entering without a warrant is posted on a door at St. Paul and St. Andrew United Methodist Church while a person waits to go inside to the church in New York City, U.S., January 23, 2025. REUTERS/Eduardo Munoz

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People gather during a service at Starting Point Community Church, which assists members of the newly arrived migrant community, amid concerns of intensified immigration enforcement by U.S. Immigration and Customs Enforcement (ICE) after the inauguration of U.S. President Donald Trump, in Chicago, Illinois U.S. January 26, 2025. REUTERS/Vincent Alban

Already, some churches that once stood defiantly as safe houses for undocumented migrants are less willing to shield them this time around.

“We are not going to offer physical sanctuary,” said Rev. Seth Kaper-Dale , a pastor at the Reformed Church of Highland Park in central New Jersey, which proudly sheltered migrants during the Obama and first Trump administrations. Kaper-Dale said he isn’t worried about Immigration and Customs Enforcement so much as right-wing extremists.

“It’s become too violent an environment, and the current president’s sort of invitation to violence makes us not want to have a label of sanctuary,” he said. “I do not need this to become the next Tree of Life synagogue,” he added, referring to the Pittsburgh synagogue where a gunman killed 11 worshipers in 2018 in the deadliest antisemitic attack in U.S. history . Just before the shooting, the assailant posted online about a Jewish agency that resettles refugees, whom he called “invaders.”

Some Christian pastors said they fully back allowing ICE authorities into churches. “We’re feeling the effects of illegal immigration in our town,” said Pastor Ken Peters in Lenoir City, Tenn.

Peters leads the Patriot Church, which has an American flag painted on the roof and about 300 parishioners. He blames fentanyl overdoses in the Knoxville region and some gang activity on people in the country illegally. Fentanyl and other drugs are often ferried across the southern border hidden in secret compartments of vehicles.

“My pastor friend group, we’re 100% in favor of Trump and his policies,” Peters added. “If you love America, then you shut the door and let in people who are good for our country and not dangerous to it.”

Still, he said, of ICE arrests, “I would pray they don’t do it in the middle of a church service. That would be pretty disruptive.”

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A man attends a service at Starting Point Community Church, which assists members of the newly arrived migrant community, amid concerns of intensified immigration enforcement by U.S. Immigration and Customs Enforcement (ICE) after the inauguration of U.S. President Donald Trump, in Chicago, Illinois U.S. January 26, 2025. REUTERS/Vincent Alban

Immigration and religion have long been intertwined in America. Many of the refugee-resettlement organizations in the U.S. are religious organizations. And the modern-day sanctuary movement goes back to the 1980s, when churches opened their doors to undocumented new arrivals from Central America—shielding them from authorities and helping them get on their feet.

Rev. Jim Rigby of St. Andrew’s Presbyterian Church in Austin, Texas, which has been sheltering a Guatemalan mother and son for nearly a decade, said it is a religious calling to protect refugees. Beyond that, he feels a particular responsibility toward those from Central America, where U.S. involvement in wars in the 1980s helped fuel destabilization.

“The immigration problem didn’t start with this generation of immigrants,” he said.

On Thursday, at the Lake Street Church in Evanston, Ill., Rev. Michael Woolf was standing firm.

The church has already been housing a family from El Salvador for about 10 years, and Woolf, the senior minister, vowed to offer short-term sanctuary to migrants during high enforcement from ICE. Built in 1873, the church has space for up to 50 people in the fellowship hall. He said he is willing to get arrested to protect them.

“If someone tries to get in here, I’m not going to stand aside. That’s not in my DNA,” said Woolf, the 34-year-old author of a book on the sanctuary movement.

Woolf said he is in touch with dozens of pastors who are willing to support efforts to protect and shelter migrants amid the new deportation push by the Trump administration—but very few are willing to house them inside their churches.

The Department of Homeland Security said Tuesday the policy change would empower authorities who were thwarted. “Criminals will no longer be able to hide in America’s schools and churches to avoid arrest. The Trump Administration will not tie the hands of our brave law enforcement, and instead trusts them to use common sense,” the agency said.

Uncertainty now clouds the New Sanctuary Movement of Philadelphia, whose 33 mostly Christian and Jewish congregations include several that sheltered 14 migrants during the first Trump administration. The group’s co-director, Peter Pedemonti , said he doesn’t know whether they would do so now.

“We’re still checking with our members about where folks are at,” he said. One unknown is whether migrant families would still turn to churches given the new policy. “It’s really the family who’s taking the bigger risk and is so much more vulnerable,” he said.

Mixed views from evangelicals

Trump’s immigration orders could put the president at odds with some of his strongest supporters. In the last election, exit polls showed 81% of white evangelical Protestants voted for him, the nonpartisan Public Religion Research Institute said. Trump also drew the support of 63% of Hispanic Protestants and 60% of white Catholics.

He got high marks from evangelical voters just before his current term started, according to a Wall Street Journal nationwide poll conducted earlier this month.

Evangelical and Catholic groups in recent days have acknowledged the need for border security and enforcement of laws, while also raising concerns about ICE having the greenlight to go into churches.

“All people have a right to fulfill their duty to God without fear,” the U.S. Conference of Catholic Bishops said about the Trump administration’s policy change.

The National Association of Evangelicals on Wednesday called the new directive allowing immigration enforcement in houses of worship troubling. “Even the announcement of this policy has caused fear, deterring some from attending church,” it added.

Galen Carey , the association’s vice president of government relations, said the group doesn’t have a position on sheltering migrants, and that isn’t its focus in speaking out about the policy. “Our goal is for people to be able to come freely to church and worship, and to become better citizens,” he said.

Immigration emerged as a potent issue in the November election, second only to the economy, polls showed, and many voters felt the influx of new arrivals strained their communities.

Lance Wallnau , a prominent leader in a fast-growing evangelical movement that has backed Trump and called for engaging in politics as a form of “spiritual warfare,” applauded the president for giving immigration authorities a freer hand.

“I’m supportive of ICE going into wherever there’s a threat to the American citizen,” he said.

Across denominations, Wallnau said he sees a divide: churches aligned with Trump’s agenda versus “woke churches” that have been “co-opted by the left.”

“Those kinds of churches aren’t going to get a sympathetic pass,” he said, “because what they’re doing is harboring and protecting people that shouldn’t be protected.”

Write to Scott Calvert at scott.calvert@wsj.com , Kris Maher at Kris.Maher@wsj.com and Joe Barrett at Joseph.Barrett@wsj.com