For a year and a half, the migrant shelter run by Our Lady of Guadalupe Parish in Logan Heights was regularly at capacity, a bridge for recently arrived asylum seekers looking to settle in San Diego.

But that number plummeted when President Donald Trump ended the CBP One appointment system, which had allowed undocumented immigrants to schedule asylum screenings at ports of entry. By March, only two people from Venezuela were left at the shelter, and they eventually left the county.

Earlier this month, the shelter suspended operations.

“I’m a little sad, honestly,” Pastor Scott Santarosa told parishioners following last weekend’s Sunday Mass, thanking those who once donated blankets, food or volunteer services. “But we have to adapt to new situations.”

Likewise, the county’s two major migrant sheltering agencies gave notice that they will be laying off employees by the end of next month.

Catholic Charities in San Diego will let go of 73 employees at its two shelters, one in San Diego County and the other in Imperial County. Jewish Family Service will do the same with about 115 employees at its San Diego Rapid Response Network migrant shelter — once hailed as a national model for welcoming a large number of people.

“This decision comes after a significant decrease in the number of asylum seekers crossing the U.S.-Mexico border, driven by recent changes in federal policy,” Catholic Charities said in a statement.

“With the reduced demand for asylum services, (Catholic Charities) has made the difficult decision to close the shelter. This outcome had been anticipated, as all employees were hired on a temporary basis, with an understanding that the program could be subject to closure.”

Both Catholic Charities and Jewish Family Service secured an additional $20 million each from the Federal Emergency Management Agency’s Shelter and Services Program in August.

Jewish Family Service recently said it still has not received any of the FEMA money, which is typically paid out as reimbursements for expenses.

South of the border, a well-known shelter in Tijuana that has served migrants for nearly 40 years may also be forced to cut back services, but for different reasons. Casa del Migrante, which has been housing recent deportees lately, is now struggling to keep up with expenses after Trump suddenly suspended U.S. foreign aid programs.

Once the busiest border corridor

For most of last year, the San Diego sector was the busiest along the U.S.-Mexico border.

In February 2024, the San Diego sector recorded 31,562 migrant encounters by Border Patrol agents. Last month, there were 1,650 — an annual drop of nearly 95%, U.S. Customs and Border Protection data show.

At the height of crossings, sheltering services were in high demand. Newly arrived migrants were processed by Border Patrol, given a court date, and then released at a public transit station in south San Diego. Others, typically more vulnerable migrants, were placed in shelters. The vast majority of migrants traveled on to final destinations across the nation, and local organizations stepped up to help get them there.

Border crossings began to fall after then-President Joe Biden issued an executive order in June limiting who could be screened for asylum at the border and instituting stricter screening standards.

So far in fiscal 2025, which began Oct. 1, the San Diego sector has recorded about 43,000 apprehensions — a 70% drop from the same period last year, San Diego Sector Acting Chief Patrol Agent Jeffrey D. Stalnaker said at a news conference last Friday.

Border officials said that they have seen an average of 30 to 40 migrant encounters a day lately. Last year, there were days border agents encountered more than 1,500, officials said.

The chief highlighted the collaboration with the Department of Defense, which has resulted in the deployment of troops to reinforce 6 miles of border barrier with concertina wire in San Diego.

“To say there has been a dramatic change would be an understatement,” he said.

Partly in response, CBP announced this month the closure of soft-sided facilities along the Southwest border that were once used to process arriving migrants — including the central processing center in Otay Mesa.

“It costs a good amount of money to be able to lease that,” Stalnaker said. “But also, since the numbers are lower, we’re able to now handle that amount of activity at our field stations.”

CBP previously closed its processing facilities in Texas and Arizona.

“The U.S. Border Patrol has full capability to manage the detention of apprehended aliens in USBP’s permanent facilities,” CBP Assistant Commissioner of Public Affairs Hilton Beckham said in a statement. “Manpower and other resources dedicated to temporary processing facilities will be redirected toward other priorities and will speed CBP’s progress in gaining operational control over the southwest border.”

The agency didn’t detail how much it cost to operate the San Diego facility, but in a news release first announcing the closures in other states, it estimated $5 million to $30 million per month for each facility.

‘Our commitment is as strong as ever’

San Diego shelters are now figuring out how to pivot to continue to serve the migrant community.

“Our commitment is as strong as ever to walk with people who are migrants, who are immigrants,” said Santarosa, the pastor of Our Lady of Guadalupe, “and especially our own immigrant people in this parish.”

Santarosa is not calling it a permanent shelter closure, but rather a suspension because “if something should change, because it’s been a very fluid situation, we would open back up and serve if a need presented itself.”

The parish is considering partnering with other groups to provide legal orientation for immigrants at the off-site shelter location in the meantime. “It feels like that could be a good use of the space because people do trust the Church, and trust is a huge thing,” he said.

Likewise, Jewish Family Service said last month when it announced the layoffs that it would shift its immigration advocacy efforts to providing pro bono legal services and community support resources.

‘Like a bucket of cold water’

In Tijuana, Casa del Migrante braced itself for months ahead of Jan. 20 for what was expected to be a higher number of deportees based on Trump’s campaign promises of mass deportations. And while deportees have been coming, the shelter — which receives 40% of its funding from U.S. government-backed foundations — did not expect to be facing a budget crisis.

But on Trump’s first day, a flurry of executive orders included a pause on foreign aid funding and a review of U.S. foreign assistance programs.

The Rev. Pat Murphy, director of Casa del Migrante, took to social media to ask for the community’s help. The U.S. funds supported operations at both the shelter and a school that provides training programs for migrants.

The nonprofit, which has been in operation since 1987, is currently relying on savings to stay open. “We’re knocking on a lot of doors to get funding from different places,” he said Monday.

Earlier this week, 60 people were staying at the shelter, most of whom had recently been deported. Before Trump took office, there were more than 100 people, mainly those waiting for their asylum appointments.

“We’re at a crisis point in terms of knowing if we’re going to be able to continue or not,” said Laura Catalina Pabón, who oversees the shelter’s funding. “Regardless of the fact that we have less population to serve, our expenses remain the same.”

Both the shelter and the nearby school have a staff of 23 people, Murphy said.

A significant portion of the funding for the Scalabrini Immigrant Training Center, which started inside the shelter in 2018 but later moved to its own three-story building in 2021, comes from foreign aid programs, said Raúl Ochoa, the school’s director of operations.

“Like a bucket of cold water,” Ochoa said. “We knew things were going to go in a different direction with President Trump coming in, but we didn’t expect this to happen so soon.”

Wilver Arteaga and Cristina Martínez, originally from El Salvador, learned about Casa del Migrante while searching for migrant shelters on Facebook. The couple arrived two weeks ago with their 3-year-old after living in the Mexican state of Coahuila for more than a year.

Their plan when they left Central America was to get to the United States. But now that asylum appointments are not offered anymore, they are hoping to stay in Tijuana until another legal path to the U.S. opens up. On Monday, the couple, who have experience as security guards, sent out résumés from their cellphones.

‘If the need arises, we’ll come back’

West of the San Ysidro Port of Entry, at a section of double-layered border fence known as Whiskey 8, what used to be a busy crossing spot for asylum seekers has grown quiet.

The last time that humanitarian workers spotted a group there was Feb. 15, said Adriana Jasso, border program coordinator for the American Friends Service Committee, who has been volunteering at the site since September 2023.

“It’s a drastic change,” Jasso said.

Last week, volunteers took stock of the numerous donated supplies stacked in clear plastic boxes in two tents, everything from food, water and medicine to clothing and shoes. One box held cellphone chargers, which a few months ago were among the most asked-for items by arriving migrants looking to contact their relatives.

Most of those items will be donated to organizations that help migrants, Jasso said.

“Maybe it’s time to step away for now,” Jasso said. “But if the need arises, we’ll come back.”

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