In the four years since its first flight, Avelo Airlines has gained loyal customers by serving smaller cities like New Haven, Conn., and Burbank, Calif.

Now, it has a new, very different line of business. It is running deportation flights for the Trump administration.

Despite weeks of protests from customers and elected officials, Avelo’s first flight for Immigrations and Customs Enforcement appears to have departed on Monday morning from Mesa, Ariz., according to data from the flight-tracking services FlightAware and Flightradar24.

According to FlightAware, the plane is expected to arrive in the early afternoon at Alexandria International Airport in Louisiana, one of five locations where ICE conducts regular flights. Avelo declined to comment on the flight and ICE did not respond to multiple requests for comment.

The airline’s decision to support President Trump’s effort to accelerate deportations of immigrants is unusual and risky. ICE outsources many flights, but they are usually operated by little-known charter airlines. Commercial carriers typically avoid this kind of work so as not to wade into politics and upset customers or employees.

The risks for Avelo are perhaps even greater because a large proportion of its flights either land or take off from cities where most people are progressives or centrists who are much less likely to support Mr. Trump’s hard-line immigration policies. More than 90 percent of the airline’s flights arrived or departed from coastal states last year, according to Cirium, an aviation data firm. Nearly one in four flew to or from New Haven.

“This is really fraught, really risky,” said Alison Taylor, a professor at the New York University Stern School of Business who focuses on corporate ethics and responsibility. “The headlines and the general human aspect of this is not playing very well.”

But Avelo, which is backed by private investors and run by executives who came from larger airlines, is struggling financially.

The money the company stands to make from ICE flights is too good to pass up, the airline’s founder and chief executive, Andrew Levy, said last month in an internal email, a copy of which was reviewed by The New York Times. The flights, he said, would help to stabilize Avelo’s finances as the airline faced more competition, particularly in and near New Haven, which is home to Yale and where the airline operates more than a dozen flights a day.

“After extensive deliberations with our board of directors and our senior leaders, we concluded this new opportunity was too valuable not to pursue,” Mr. Levy wrote in the email on April 3, a day after Avelo signed the agreement with ICE.

While the military carries out some deportation flights, ICE relies heavily on private airlines. There is little public information about those flights, which ICE primarily arranges through a broker, CSI Aviation, said Tom Cartwright, a retired banking executive who has tracked the flights for years as a volunteer with Witness at the Border, an immigrants rights group. Most are operated by two small charter airlines, GlobalX Air and Eastern Air Express, he said.

GlobalX started operations in 2021 and conducts flights for the federal government, college basketball teams, casinos, tour operators and others. It has grown rapidly and brought in $220 million in revenue last year but is not yet profitable. This year, it has operated deportation flights to Brazil and El Salvador. Eastern Air Express is part of Eastern Airlines, a privately held company.

GlobalX and Eastern Airlines did not respond to requests for comment.

Contracts for such flights provide airlines consistent revenue, and the business is much less vulnerable to changes in economic conditions than conventional passenger flights. By Mr. Cartwright’s count, which is based on a variety of sources, ICE operated nearly 8,000 flights over the year that ended in April, most of them within the United States. CSI Aviation alone was awarded hundreds of millions of dollars in ICE contracts in recent years, according to federal data.

Avelo’s decision last month to join in on those flights was met with a swift backlash.

Within days of Mr. Levy’s internal announcement, the New Haven Immigrants Coalition, a collection of groups that support immigrants’ rights, started a campaign to pressure Avelo to drop the flights. An online petition started by the coalition has gained more than 37,000 signatures. Protests also sprouted up near airports in Connecticut, Delaware, California and Florida served by Avelo.

The Democratic governors of Connecticut and Delaware denounced Avelo, while lawmakers in Connecticut and New York released proposals to withdraw state support, including a tax break on jet fuel purchases, from companies that work with ICE.

William Tong, the Democratic attorney general of Connecticut, demanded answers of Mr. Levy, who deferred to the federal government. In a statement last month, Mr. Tong called Mr. Levy’s response “insulting and condescending.”

The Association of Flight Attendants-CWA, a union that represents flight attendants at 20 airlines, including Avelo, raised concerns. The union noted that immigrants being deported by the Trump administration had been placed in restraints, which can make flight attendants’ jobs much more difficult.

“Having an entire flight of people handcuffed and shackled would hinder any evacuation and risk injury or death,” the union said in a statement. “It also impedes our ability to respond to a medical emergency, fire on board, decompression, etc. We cannot do our jobs in these conditions.”

Avelo said that under its deal with ICE, it would operate flights within the United States and abroad, using three Boeing 737-800 jets. To handle those flights, the airline opened a base at Mesa Gateway Airport and started hiring pilots, flight attendants and other staff.

In a statement, Mr. Levy, a former top executive at United Airlines and Allegiant Air, said the airline had not entered into the contract lightly.

“We realize this is a sensitive and complicated topic,” he said. “After significant deliberations, we determined this charter flying will provide us with the stability to continue expanding our core scheduled passenger service and keep our more than 1,100 crew members employed for years to come.”

The airline, which is based in Houston, said it had operated similar flights for the Biden administration. “When our country calls, our practice is to say yes,” it said in a separate statement.

In the email last month, Mr. Levy celebrated the fact that Avelo had nearly broken even in 2024, losing just $500,000 on $310 million in revenue. But the airline needs to raise more money from investors, he said. Performance this year has suffered as national consumer confidence has waned, and the airline is facing rising competition.

Avelo was seeking revenue that would be “immune from these issues,” Mr. Levy said in the email, and pursued charter flights, including for the federal government. To accommodate the ICE flights, the airline also scaled back its presence at an airport in Santa Rosa, Calif.

Avelo has raised more than $190 million, most of it in 2020 and 2022, according to PitchBook. Mr. Levy’s email said the airline hoped to secure new funding this summer.