Andrew and Debbie James are evangelical Christians. Born in England, the couple moved to Denver years ago and raised their children there. Mrs. James had a profound religious conversion experience early in parenthood, and their large nondenominational church quickly became the focal point of their lives. They used to say that if the doors were open, they were there.

“We always joked that we had this perfect little scenario,” Mrs. James said. “We had our boy, then we had our girl, and they were two years apart and they were just perfect.” They were strict parents — too strict, they say in hindsight, with the goal to “shield them from absolutely everything.”

When the couple’s older child was 19, living at home as a college student, Mrs. James got a call from the pharmacy informing her that her child’s prescription for estradiol, or estrogen, was ready. In a panic, she searched the teenager’s room, confronting her that evening.

It went badly. They initially refused to use their daughter’s chosen name, Lilia, and Mrs. James could barely be in the same room with her when she was wearing a skirt. Then a pastor at the church encouraged them to kick their daughter out of their home.

“This must be biblical advice,” she recalled thinking. “This must be what we’re supposed to do.”

‘A space of curiosity’

Many progressive and Mainline Christian congregations have moved to affirm transgender and nonbinary members. But for many conservative Christians, the rise of transgender identities in both visibility and in sheer numbers, particularly among young people, has been a profoundly destabilizing shift. Almost 90 percent of white evangelicals believe gender is determined by sex at birth, according to the Pew Research Center, compared with 60 percent of the population as a whole.

Austen Hartke realized he was transgender in seminary, where he was studying the Hebrew Bible; he came out as soon as he graduated. It was 2014, the same year that Laverne Cox was on the cover of Time magazine, and it felt to Mr. Hartke that the culture around him was steadily improving, that awareness and acceptance would go hand in hand, including in conservative spaces.

That is not what happened. If trans people in conservative churches encountered clumsiness and ignorance around issues like pronouns back then, he said, now they face outright hostility.

“If you’re afraid of change, that’s what trans people now represent,” he said.

Some Christians have fought against expanding gender norms with vociferous opposition to everything from drag shows to hormone treatments. In churches and Christian schools, transgender people have been mocked, kicked out and denied communion. Transgender young people from conservative Christian families have shared stories of being banished from homes and relationships, often with devastating effects on their mental health. In many ways, conservative Christians have become the face of the American anti-trans movement.

But in the quieter spaces of church sanctuaries, counseling offices and living rooms, there are earnest searches for understanding. Churches are hosting panel discussions and film screenings, training their youth leaders, rewriting their statements of faith, and rethinking how they label bathrooms and arrange single-sex Bible studies. Even those that continue to draw a hard line against homosexuality are sorting through new questions raised by gender identity.

In the most intimate cases, Christians are steering through agonizing, unfamiliar conflicts between their families and their God, or as some put it, between love and truth.

It is a search that echoes uncomfortable conversations in secular realms, as Americans of all political and ideological persuasions grapple with changes to deeply ingrained notions of masculinity and femininity.

And in a landscape in which furious rhetoric blazes through statehouses and across social media, some are staking out a kind of middle ground. It is one that takes seriously the moral and theological concerns shared by many Christians, and refuses to set them aside. But it also guides them to accept the reality of gender dysphoria, or distress over one’s sex, and to remain open to a spectrum of outcomes.

Julia Sadusky, a psychologist in Colorado, is one of relatively few expert voices who has stepped into that fraught territory between anti-trans fear and zeal on the right, and what some see as a progressive orthodoxy on the left that leaves little space for parental doubts. Her degrees are from conservative Catholic and evangelical universities, and these days, she spends most of her time speaking with conservative Christians in intimate settings. In her private practice in a suburb of Denver, she sees bewildered and sometimes angry clients whose children have told them they are transgender or nonbinary.

When parents ask if she can steer their child away from a transgender identity, she declines and guides them to consider accompanying their child through a range of paths from there. She has clients who have transitioned socially, and who have pursued medical transition, although she acknowledges having concerns about potentially irreversible medical interventions on teen patients in particular.

She also addresses audiences of churchgoers attempting to process tectonic cultural shifts around them. Many of her listeners have received alarming and sometimes false messages about those shifts from conservative media and word of mouth.

On a rainy Sunday afternoon last summer, Dr. Sadusky was in New York City, onstage in a former Elks Lodge in Queens, leading a roomful of evangelical Christians through a slide show about gender identity.

“I’m inviting you into a space of curiosity as opposed to judgment,” she told the crowd of about 100 people at New Life Fellowship church. Some of them jotted down notes. Others snapped photos of her slides — with lists of terms like “demigender” and “agender,” and charts of rocketing rates of transgender identity among young people.

She encouraged attendees to use other people’s preferred pronouns, explained why she does not like loaded terms like “social contagion” and discouraged pat catchphrases like “God doesn’t make mistakes.”

“None of us are God here,” she said. “But we do need to answer to him.”

‘Is there no truth?’

The theological foundation of Christian opposition to the concept of transgender identities announces itself in the first chapter of Genesis. “So God created mankind in his own image, in the image of God he created them,” the passage reads. “Male and female he created them.”

Christian advocates for transgender people point out that the Bible depicts a surprising range of gender diversity without apparent judgment. Jacob, a patriarch of the nation of Israel, is described as a “smooth” young man who stays in the family’s tent and is favored by God over his more traditionally masculine brother, the hunter Esau. Jesus says in the Gospel of Matthew that some men are born eunuchs.

But in the New Testament, mostly in the writings of the Apostle Paul, several passages lay out distinct roles for men and women. Women are to cover their heads in church and submit to their husbands; men are to lead their families and love their wives. Though they are debated by scholars and ordinary Christians, these texts have profoundly shaped the family structures, career paths and spiritual lives of billions of people around the world.

For some Christians, then, the rise of transgender identities poses a blunt danger, potentially undermining family stability, definitions of truth and authority structures they have built their lives around. As parents, conservative evangelicals tend to prioritize keeping children in the fold rather than encouraging them to push boundaries. Many evangelical parenting resources emphasize obedience and authority, with the goal of raising children not to “find themselves” but to carry on traditions.

“You can see something happening that’s shaping how we understand the nature of the human person,” said Mary Rice Hasson, a senior fellow at the conservative Ethics and Public Policy Center, where she directs a program whose aim is in part to help parents “counter gender ideology.”

Ms. Hasson, who is Catholic, described recent cultural shifts around gender as upending fundamental assumptions about the universe: “Can you trust your senses? When you see something, can you name it, does it have an objective reality? Or is there no truth?”

The gender issue has also thrown new fuel on smoldering debates over sexual orientation, which have divided multiple Christian denominations and institutions for decades. Those disputes had largely cooled in the wake of the Supreme Court decision in Obergefell v. Hodges, which made same-sex marriage legal across the country. But the less-settled landscape on gender issues has prompted new confrontations and disagreements, and revived older debates about sexuality.

Some conservative evangelical churches have turned to a document called the Nashville Statement to help them navigate the theology of contemporary gender identity. The statement, crafted by leaders of the conservative Council on Biblical Manhood and Womanhood in 2017, initially made headlines as a document that articulated a sharp position against homosexuality and same-sex marriage.

But its writers also address gender identity, stating that God enables people to “forsake transgender self-conceptions” and to “accept the God-ordained link” between their biological sex and their gender.

Denny Burk, the president of the Council on Biblical Manhood and Womanhood, who helped write the statement, said that the most urgent matter for Christians in the public sphere now is bringing clarity to foundational questions about what it means to be human — questions that trace back at least to the sexual revolution, and were accelerated, as he sees it, by the Obergefell decision. “What does it mean to be a person, and in particular what does it mean to be male and what does it mean to be female?” he said. “You’re seeing Christians having to articulate what used to be assumed.”

Mark Yarhouse, a clinical psychologist who heads the Sexual and Gender Identity Institute at evangelical Wheaton College, has identified three broad frameworks through which Christians tend to see gender identity: On one end of the spectrum is the traditional conservative view that asserts that male and female are God-ordained categories to which people must conform. On the other is a celebratory embrace of new identities.

In the middle is a view that diversions between gender identity and biological sex are an unfortunate departure from the norm but not a moral failure.

Dr. Yarhouse said at least 80 percent of the speaking and consulting requests he gets now pertain to gender identity rather than sexuality, where his career began. “This is a wave that is going to crest over the evangelical church, and the church is not ready,” he said.

‘We have to allow for questions.’

Finding a foothold for compromise within such a stark landscape can feel impossible, and even the notion of “compromise” is offensive to many. That is why many Christians with nontraditional gender identities end up leaving their conservative churches.

“I never wanted to be away from God; it was just that God’s people scared me to death,” said Lesli Hudson-Reynolds, who is nonbinary and gay. Raised Southern Baptist in Texas, and active in ministry in college, they were essentially pushed out of the church when they came out as a lesbian. (Mx. Hudson-Reynolds uses they/them pronouns.)

Things began to change when their wife died in 2009, and a local evangelical pastor agreed to host and pay for her funeral without question. The church treated Mx. Hudson-Reynolds with respect, as a grieving spouse. “I hadn’t been treated like a human being by Christians in a very long time,” they recalled. That began their path back to the church.

Mx. Hudson-Reynolds’s own views on gender and sexuality have evolved. They have chosen to be celibate going forward, and consider themselves a “Side B” Christian, a term developed by gay Christians who believe the Christian life requires them to abstain from sexual behavior outside traditional, heterosexual marriage but reject the notion that all L.G.B.T.Q. people can or should become straight.

“A lot of Christians call you a heretic, and a lot of gay people call you a traitor,” said Mx. Hudson-Reynolds. They went on to work for Posture Shift, an organization that consults with pastors and parents with the goal of making churches and homes “safe for LGBT+ family and friends.”

Dr. Sadusky often recommends Posture Shift’s resources to her clients, including its guidebook for families, which added new material on gender in its latest edition.

The questions Dr. Sadusky said she hears from parents with transgender children in her private practice are immediate and personal: Does this mean I won’t have grandchildren? (“That’s the No. 1 thing they’re worried about.”) If they don’t immediately affirm the child’s identity, they worry their child will be told the parents are irredeemable bigots, cut off the relationship, or even that the child will take their own life.

Once a month, Dr. Sadusky leads a group discussion by video chat for other therapists to seek peer advice on challenging cases. On a Friday afternoon last spring, a group of six counselors from across the country, most of them Christians who work largely with Christian clients, had gathered. (The counselors allowed a reporter to sit in on the meeting on the condition that they would not be named and that no identifying details of their cases would be shared.)

A marriage and family therapist in the Mountain West presented the first case: a family in which the parents were strongly resisting their older teenage child’s desire to publicly present herself as female, refusing to use her new pronouns because they view it as “lying,” and thus a betrayal of their faith. The counselor felt stuck; the parents’ objection was a barrier to maintaining a relationship with their daughter, but it was so deeply rooted in their values that it was hard to see how they could set it aside.

The idea that using preferred pronouns might be “lying” is common for some Christians, Dr. Sadusky told the therapist. She suggested proposing to the parents that they think of using their daughter’s preferred pronouns not as a statement of belief but as a form of hospitality, a concept from Gregory Coles, the author of “Single, Gay, Christian.” Compare it to being a missionary in a Muslim country, Dr. Sadusky offered: You would probably use the term “Allah” for God in that context, for the sake of staying in conversation.

Over the course of Dr. Sadusky’s decade-long career, she has seen rapid shifts in the way her clients view their own gender identity. She now sees fewer people who report longstanding distress and more who say a version of, “It’s not distressing, it’s who I am and I want to make these modifications,” she said.

Most people, including conservatives, she said, are fairly comfortable with the idea of an adult who was raised male, say, and began to understand herself as female early in childhood with little relief over many years. Those people might have differing opinions about the proper responses to that kind of distress, but they are not as threatened by its existence as a phenomenon experienced by a small minority of individuals.

The larger threat to many conservatives, she said — and one she would like to challenge — is the notion that responding compassionately to such distress means disregarding all beliefs about differences between men and women.

This is not an altogether satisfying approach for many progressive Christians, who view Dr. Sadusky’s balancing act as not going far enough to fully embrace L.G.B.T.Q. people.

“I think of it as being a harm-reduction strategy,” said Mr. Hartke, who came out as trans after seminary and went on to found Transmission Ministry Collective, an organization that supports transgender and “gender-expansive” Christians. If Mr. Hartke is talking with parents who are dead set against their child’s transgender identity, he sees Dr. Sadusky’s work, in particular her books written with Dr. Yarhouse, as a resource that “moves them along from where they were to a place that can be less harmful.”

But Mr. Hartke, who is active in a Lutheran church, said he would prefer that Christians listen most intently to transgender doctors, scholars and psychiatrists, who combine experience and expertise.

The notion that the very categories of “man” and “woman” will someday be erased strikes Mr. Hartke as far-fetched. But he sees an analogy between explorations of gender and of faith.

“If we actually want people to feel solid in their identity,” he said, “we have to allow for questions in the same way that if we want people to feel solid in their faith, we have to allow for questions about their faith.”

‘We were good little soldiers.’

Andrew and Debbie James defied their pastor’s advice to kick their daughter out of their house.

But Lilia moved out anyway, frustrated by her restrictions in the home. Her parents began reading, including books by Dr. Yarhouse and by David Gushee, a Christian ethicist who has argued for rethinking traditional Christian approaches to inclusion. They prayed. And they participated in a support group through Embracing the Journey, a network of small groups intended to “build bridges” among L.G.B.T.Q. people, their families and the church.

The group’s founders, Greg and Lynn McDonald, live near Atlanta and have a son who is gay. Their first reaction when he came out, informed by groups like Focus on the Family, was that his sexuality was a sin, and one that had been caused by a failure in the home — an absent father or an overbearing mother. They changed their approach after reading the gospels together, paying attention to the Bible’s accounts of how Jesus actually treated people.

“I felt I needed to choose: Choose God or choose my son,” Mrs. McDonald recalled. “God told me, ‘No, you get to do both.’”

The McDonalds said almost half of the families that participate in Embracing the Journey now come to them because they have children who are transgender or nonbinary, like the Jameses. Eventually the Jameses started leading groups for other parents; they have now led at least five groups, counseling more than 100 parents.

Lilia James is now 25 and lives in Wisconsin. She has a strong relationship with her parents. She got engaged in June before a trip to Colorado with her girlfriend, and they have contemplated getting married at the same courthouse where her parents married.

“It was a fight between loving their child unconditionally or believing and following what their religion was telling them,” she said on a video call last summer from her parents’ back porch. “For a long time it seemed like those two things were at odds and they would have to pick.”

She added: “I’m so proud of them.”

Like many conservative Christian families with children with gender distress, the Jameses eventually left their church. They sometimes stream services at a church they like in Atlanta, and occasionally try attending local congregations that affirm L.G.B.T.Q. relationships and identities. They remain strongly committed to their faith but do not consider themselves as having a “church home.” Their worries now are about the political climate hostile to their daughter, and the fact that both their children have walked away from Christianity.

For so long, “we were good little soldiers,” Mrs. James said. Now, “we live in the gray.”