Bishop Mariann Edgar Budde was nearing the end of her sermon for the inaugural prayer service on Tuesday when she took a breath and looked directly at President Donald J. Trump.

“I ask you to have mercy upon the people in our country who are scared now,” said Bishop Budde, the leader of the Episcopal Diocese of Washington. “There are gay, lesbian and transgender children in Democratic, Republican and independent families, some who fear for their lives.”

The direct appeal to Mr. Trump, at the start of the first full day of his presidency, was a remarkable moment. Twenty-four hours after he had reclaimed the highest office in the land, summoning tech billionaires as witnesses and pulling off a sweeping display of power by signing of a flurry of executive orders, he was suddenly confronted by an extraordinary act of public resistance from an unlikely source: a soft-spoken bishop.

“The vast majority of immigrants are not criminals,” Bishop Budde said. “I ask you to have mercy, Mr. President, on those in our communities whose children fear that their parents will be taken away, and that you help those who are fleeing war zones and persecution in their own lands to find compassion and welcome here.”

Mr. Trump, seated in the first row of pews in the towering Washington National Cathedral, looked down and then away. Vice President JD Vance raised his eyebrows and looked several times at his wife, Usha Vance, who kept her gaze trained ahead on the bishop. When Bishop Budde finished, Mr. Trump said something to Mr. Vance, who shook his head in apparent irritation. Members of the Trump family seated directly behind them appeared to look at one another, noticeably perturbed. Eric Trump, Mr. Trump’s middle son, shook his head.

It was not how Mr. Trump has generally been spoken to as he returns to the White House. Since winning the election, he has been courted by powerful business leaders and politicians alike, including many who kept their distance during his first term. Just the day before, he celebrated his return to office with an inauguration in the Capitol Rotunda, a rally surrounded by supporters and a succession of inaugural balls. Even former President Joseph R. Biden Jr. greeted Mr. Trump at the White House by saying, “Welcome home.”

Bishop Budde’s comments came a day after Mr. Trump issued a flurry of executive orders focused on transgender rights and immigration.

The appeal by the pastor clearly grabbed Mr. Trump’s attention. Asked by a reporter what he thought of the service, the president said: “Did you like it? Did you find it exciting? Not too exciting, was it?

“I didn’t think it was a good service, no,” Mr. Trump continued. “They could do much better.”

In an interview, Bishop Budde said she had decided to speak to the president directly because “of the fear that I have seen and experienced among our people — people that I know and love, both within the immigrant community and within the L.G.B.T.Q. community, and how terrified so many are.”

She said she was concerned about “the level of license to be really quite cruel” that some people feel now.

“I wasn’t necessarily calling the president out. I was trying to say, ‘The country has been entrusted to you,’” Bishop Budde said. “And one of the qualities of a leader is mercy, right? Mercy. And to be mindful of the people who are scared.”

Bishop Budde is not the only prominent clergy member to call attention to the fear caused by Mr. Trump’s agenda. Pope Francis on Sunday called Mr. Trump’s plans for mass deportations “a disgrace.”

Mr. Trump began his presidency on Monday with executive actions that aimed to turn his campaign rhetoric into tangible policies, including one that rescinded a Biden administration order that sought to prevent discrimination on the basis of gender identity or sexual orientation.

Mr. Trump’s new order, the administration said, seeks to defend women against “gender ideology extremism” that allows biological males to undermine their rights and privacy. And the definitions it sets forth go further to more explicitly define “sex.”

Under the order signed by Mr. Trump on Monday, males and females would be defined at “conception,” the text states. Someone who eventually produces “the large reproductive cell” would be deemed female, the order says. A male would be defined as the person who eventually “produces the small reproductive cell.”

The order also says that the federal government would no longer recognize “gender identity,” and only “sex” as defined by “an individual’s immutable biological classification as either male or female.”

The order also prohibits the use of federal funds for any promotion of “gender ideology” through grants or other government programming, as well as the use of public funding for transition-related medical procedures in prisons.

The order effectively defines transgender Americans out of existence.

“At its core, this executive order is an appallingly cruel effort to make transgender people strangers to the law and push them back into the closet,” said Sarah Warbelow, legal director at the Human Rights Campaign.

Mr. Trump also issued multiple immigration-related executive orders on Monday that suspended refugee admissions, severely restricted asylum for migrants and made clear that he intended to deploy the military to the southern border. The border, however, remains relatively calm after a record number of illegal crossings earlier in the Biden administration.

The Trump administration also rescinded a Biden policy that directed Immigration and Customs Enforcement agents to not make arrests at schools, places of worship and other places described as “sensitive locations.”

Throughout his campaign, and during his first term, Mr. Trump often portrayed all migrants crossing the border illegally as criminals. While sporadic crimes by migrants have gained national attention in recent years, homeland security officials themselves acknowledge that most people crossing the border are fleeing poverty or violence and seeking a better life.

“There are times when he talks of immigrants in broad strokes that feel as if the image portrayed is that all immigrants who are coming into the country are dangerous,” Bishop Budde said. “And I know that’s not true. It’s not true.”