Since the blockbuster musical “Hamilton,” tourists have been swarming Trinity Church, part of an Episcopal parish in Lower Manhattan that dates to the 17th century. Alexander Hamilton and his wife, Eliza Schuyler Hamilton, are buried in the cemetery there.

Recent years have been good to the church and the rest of its campus. St. Paul’s Chapel, near the World Trade Center, escaped destruction during the terrorist attacks of Sept 11, 2001, and now gleams following a fresh coat of paint. After a cleaning in September, Hamilton’s white marble obelisk also sparkles. Soon the entire church — and a new $350 million glass tower under construction behind it — will, too.

It makes sense. If a founding father can get a 21st-century update, so can the church where he is buried. Especially since the church in question is very, very rich.

While many places of worship are warding off developers as they struggle to hold onto their congregations and buildings, Trinity is a big-time developer itself.

The church has always been land-rich. And it has long had its own real estate arm, which controls ground leases and office space rentals in the buildings it owns. But now it finds itself with a newly diversified portfolio worth $6 billion, according to the current rector, the Rev. Dr. William Lupfer.

After being instrumental in changing the zoning laws in Hudson Square, a neighborhood between West Houston and Canal Streets, Trinity Real Estate has entered into a joint venture that gives it a majority stake in 12 buildings that contain six million square feet of commercial space. A lucrative deal with the Walt Disney Company, valued at $650 million, was signed just last year.

And as it builds its glass tower — which will house administrative offices, public gathering spaces and, yes, commercial tenants — Trinity is also renovating the interior of its historic church, which is expected to cost $110 million.

Trinity has been able to do all this because it’s been a savvy manager of its resources. It is also, as a church, exempt from taxes.

But some wonder about the ethics of a religious institution being such a power player in the world of New York real estate.

“What is the fundamental economic issue going on that churches deserve tax exemption and can build up a lot of wealth?” asked Rachel M. McCleary, a lecturer in the economics department at Harvard University and co-author of the coming book “The Wealth of Religions: The Political Economy of Believing and Belonging.”

Trinity’s current affluence can be traced to a gift of 215 acres from Queen Anne in 1705. (The church was first chartered, under King William III, in 1697, a few decades after the British took over New Amsterdam.) Trinity still owns 14 acres of that original land grant, mostly in Hudson Square.

At the time Trinity received the land, of course, there was no separation of church and state. “They were a favored religion, and that gave them a leg up,” Dr. McCleary said. “The question becomes, How are they to be viewed in a pluralistic religion market, and what is their response in that market today?”

Patti Walsh, a spokeswoman for the church, wrote in an email that Trinity handles such a market by working closely with other organizations to help them further their mission. “We currently work with many partners in New York City and around the world to build neighborhoods, to help develop clergy and lay leadership for the church, and to help our partners resource their ministries.”

The current Trinity is the third church to be built at Broadway and Wall Street. Designed in a Gothic Revival style by Richard Upjohn and completed in 1846, the brownstone building was the tallest structure in the city for decades, and one of the first to be declared a landmark.

It’s “a place where you can get away from the noise and experience the aesthetic beauty and quiet,” said the Rev. Phillip A. Jackson, the vicar of the Episcopal parish of Trinity Church Wall Street.

But now that the church is at the center of the development boom in Lower Manhattan, it’s less of an oasis of calm and more of a contributor to the very noise and disruption from which longtime residents have sought a reprieve.

There is the new tower, which topped out late last year, and will have 17 floors of office space in addition to a nine-story base devoted to parish and community use.

And as part of the church interior’s “rejuvenation,” as the parish leadership calls it — the first extensive renovation in decades — the nave is closed and scaffolding reaches to the 65-foot-high ceiling so that conservation experts can inspect stained-glass windows and the integrity of the ceiling. There will be three new organs, ergonomically contoured seats for the old oak pews and stained-glass pendant lights that will be controlled by an iPad. The church’s famous altarpiece, donated by the Astor family, will be restored and placed on rails so it can be moved back and forth depending on the type of service or event.

The project, overseen by Murphy Burnham & Buttrick Architects, which restored St. Patrick’s Cathedral in Midtown, is a shining example of stewardship. The New York Landmarks Conservancy awarded Trinity a prestigious Chairman’s Awards last year.

These projects stand in stark contrast to other houses of worship around the city, many with dwindling congregations, struggling to pay heating bills and keep the roof from leaking.

Indeed, a section of falling ceiling was one of the latest indignities suffered by the Metropolitan Community United Methodist Church, in East Harlem, built in the Gothic style in the 1870s. It is now slated for demolition after the pastor, the Rev. Dr. Richard N. Hayes, gave up on the structure following years of “repair, repair, repair,” he said.

Dr. Hayes has struck a deal to sell the church, which is not a landmark, to a developer — a plan that will provide money for a new church to be built on an adjacent lot. The likelihood that the developer will raze the historic building has divided the congregation and prompted an outcry from neighbors and preservationists.

“For decades the preservation of churches has been a major issue,” said Andrew Dolkart, a professor at the Columbia University Graduate School of Architecture, Planning and Preservation. No longer. “It’s become a crisis,” he said.

Although attention in recent years has focused on the shuttering of churches by the Roman Catholic Archdiocese of New York, the problem affects all denominations, said Peg Breen, president of the New York Landmarks Conservancy, which is surveying religious properties in the five boroughs.

Congregants have resorted to doing patchwork repairs themselves; pastors solicit donations in emergencies. Recently, after the front door blew off the Immanuel- First Spanish Church in the Boerum Hill neighborhood of Brooklyn. It was rehung, but remains irreparably damaged. A replacement will cost as much as $9,000, said the Rev. Dr. Hector B. Custodio, known to all as Pastor Benny. So far, he has collected $1,200.

Many religious leaders have become experts in applying for grants and organizing capital campaigns.

“We learn none of this in seminary,” said the Rev. Anne Sawyer, rector of St. Mark’s Church-in-the-Bowery, which is trying to raise money to replace faulty copper gutters that funnel rainwater into the building.

But sometimes the tactic works. The Church of St. Anselm and St. Roch, for example, a domed Byzantine Revival structure in the South Bronx, recently received a $40,000 grant from the Landmarks Conservancy.

Some churches have allowed developers to build on their property. Residents of Morningside Heights in Upper Manhattan were still recovering from an apartment tower being erected on the campus of St. John the Divine in 2008, when the church gave the go-ahead for a second project — to be built just steps from the landmark cathedral, in 2015.

And then there is the sale of air rights. Under the new East Midtown zoning laws, landmark religious institutions are able to transfer air rights (the space over their buildings) to developers who can apply those air rights within a 78-block area. St. Patrick’s, St. Bart’s and Central Synagogue, which supported the new rules, are all expected to sell their air rights.

The New York religious institutions that are safest from destruction, it seems, have either been declared landmarks or are land-rich. Trinity Church is both.

In 2005, Trinity hired Carl Weisbrod, an urban planning expert, director of the Lower Manhattan Development Corporation and founding president of the Alliance for Downtown New York, to lead the church’s real estate arm. Mr. Weisbrod initiated the 2013 rezoning of Hudson Square, which allowed for the construction of residential buildings. This set off a frenzy of development in the area and greatly enhanced the value of Trinity’s holdings.

Trinity then diversified, entering into a joint partnership with Norway’s Norges Bank Investment Management that involved the church’s holdings in Hudson Square.

Since 2015, proceeds from the partnership have totaled $1.73 billion and have been folded into a range of other investments. In 2017, the latest year for which an audited financial statement is available, Trinity’s portfolio yielded a net return of $301 million.

Trinity’s wealth enables it to support other churches (it has its own grant department with a formal application process). It has given away $10 million a year and plans to ramp up its contributions, according to the church spokeswoman, Ms. Walsh. It also finances its own humanitarian efforts, including a 325-unit affordable residence for older people and those with disabilities, as well as brown-bag lunches for 35,000 annually.

About six years ago, nearly half of Trinity’s vestry — a group of parishioners who function like a board of directors — resigned because they felt the church wasn’t doing enough to help those in need. But two congregants who were part of the upheaval — including Jeremy C. Bates, who filed a lawsuit that led to the institution making its financial records public — believe the church has turned a corner. “I feel we are more unified,” Mr. Bates said.

There is a point to be made about the importance of paying attention to the bottom line. Abyssinian Baptist Church in Harlem, a New York City landmark with a nonprofit real estate arm that focuses on affordable housing and community development, overextended itself and was forced to sell off properties to satisfy debts.

“We were just trying to do good where others were not doing it,” said the Rev. Dr. Calvin O. Butts III, pastor of the church. “We did what we could, hit a bump, and had to sell off real estate.”

Dr. Lupfer sees the new Trinity tower as a “ministry tool” for his congregation and considers its costs part of its mission spending. Trinity’s website describes the project, rather modestly, as a “new parish building.”

But it is considerably more than that, and the development process has not been without controversy.

Trinity’s original proposal — a modernist design by Pelli Clarke Pelli Architects replacing a pair of smaller buildings from the 1920s — was to include luxury apartments.

It did not go unnoticed.

“When Trinity Church announces it has got to take down buildings that may have had some attraction for the neighborhood and replace them with something almost double in size and mostly residential, some people may have looked at a religious institution and asked questions they may not have asked of a commercial developer,” said Anthony Notaro, the chairman of Community Board 1, covering the area south of Canal Street.

To its credit, say members of the community, the church invited the public to weigh in on the plan for the tower’s podium, holding a series of workshops in St. Paul’s Chapel.

As a result, art studios and public gathering spaces were added to the tower’s base, which will also contain a Sunday school, a basketball court and a computer lab.

“Like a 92nd Street Y,” said Reverend Jackson, referring to the popular cultural center on the Upper East Side. Trinity expects to move into its new offices this fall, with the public spaces opening the spring of 2020. The church plans to reopen this Christmas.

Trinity appears to have it all: a vibrant congregation, well-tended church buildings, a shiny new tower promising robust amenities — and abundant resources.

In some respects it might even resemble the megachurches of the suburbs, with their broadcasting stations and satellite churches to which they beam the Sunday service. Trinity’s own broadcast room is being updated in the renovation, as are other back-of-house spaces. A large split-screen monitor in the new sacristy will allow the clergy to track activity in the sanctuary as well as in St. Paul’s and in the parish-house portion of the new tower.

Could big, muscular churches become the new normal in New York as smaller churches vanish?

The Rev. Dr. Donna Schaper, of Judson Memorial Church in the West Village, certainly hopes not. Smaller houses of worship provide not only the beauty of their historic structures, she argued, but also crucial social services as well: soup kitchens, food pantries, art programs and gathering places for community meetings.

“We need help — technical assistance, policy relief,” Dr. Schaper said. She maintains it is a mistake when churches get into the real estate game on their own. The sale of air rights, she pointed out, has led to “gentrification and its partner, racism,” as demolished religious institutions are replaced by luxury housing, often resulting in the displacement of longtime neighborhood residents.

Judson Memorial, designed by Stanford White in the Romanesque style, with stained glass by John La Farge, is a designated city landmark and is listed on the National Register of Historic Places. The church is putting on a new roof after a $3 million fund-raising campaign, but it must turn around and raise $4 million more because it has heating issues and a broken elevator.

The elevator is a serious concern, since the church has removed the pews in the sanctuary to allow for “hyperuse,” as Dr. Schaper put it, by a variety of groups. Because these rentals yield important revenue — they make up over a third of Judson’s $1 million annual budget — worship services now take place on the second floor. Judson provides services to 150 undocumented immigrants a week, among others.

Dr. Schaper has started a movement called Bricks and Mortals, with the goal of coming up with collective solutions so that no church has to go it alone. One idea is for the city to create an air-rights bank that would allow the rights “to be monetized, but not abused” — put into a bank for the development of affordable housing, for example.

“My fear is that the very thing that makes New York so lovely and interesting — the variety of our culture — is threatened by congregations becoming restaurants and high-end apartments. It’s almost as tragic as losing the beautiful buildings.”

Susan Beachy contributed research.

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