Elizabeth J. McCormack, a former Roman Catholic nun who was the catalyst for sweeping changes at Manhattanville College in the 1960s and ’70s, and who later advised major foundations on philanthropic strategies, died on Friday at her home in Manhattan. She was 98.

Her grandson Nicholas Arons confirmed the death.

In recent decades Ms. McCormack had been one of the nation’s most influential philanthropic counselors, guiding the Rockefeller family, the John D. and Catherine T. MacArthur Foundation and other donors on the arts of humanitarian giving.

But she was best known to an earlier generation as the audacious president of Manhattanville, an independent liberal arts college in Purchase, N.Y., in Westchester County, from 1966 to 1974. She oversaw Manhattanville’s transformation from a women’s college to a coeducational institution. It was an era of cultural turmoil, when the relevancy and even the survival of small Catholic women’s colleges were in doubt.

To many traditional Catholics, Ms. McCormack had some unthinkable ideas. She recognized a contradiction in a college culturally bound to church traditions but dedicated to intellectual freedom. And in what the church regards as a cardinal sin but what she called compassion, she quietly advised a student on how to obtain an abortion.

Ms. McCormack was a nun for 30 years, but as she came to question church teachings on a number of issues she obeyed her conscience and left her order, the Society of the Sacred Heart. At 54, she married a divorced Jewish father of five children.

In her eight years as the college’s president, she never kept a paycheck, secretly turning each one over to her order. Later, as an adviser to philanthropies on the distribution of vast fortunes, she earned millions of dollars in salary herself and gave much of it away.

“I think now in retrospect I didn’t want the life that I would have had, had I not become a nun,” she told Charles Kenney for his book “No Ordinary Life: The Biography of Elizabeth J. McCormack” (2012). “I actually, from many points of view, had a much fuller life. I had a career. I was educated. I learned leadership. It really gave me an awful good life.”

Founded by a Catholic religious order as an academy for women in 1841 and reorganized as a college in 1917, Manhattanville College of the Sacred Heart had long been a school of choice for young women from affluent and middle-class Catholic families. Rose Fitzgerald Kennedy and some of her daughters and daughters-in-law were among the graduates.

While not funded or controlled by the church, the college had always been identified with Roman Catholicism. Prayer and Masses were elements of life. Gregorian chant was a required course. Many teachers were Sacred Heart nuns. Ms. McCormack, a 1944 Manhattanville graduate, wore the order’s black habit for much of her presidency.

But to win state and federal grants, as well as more students, single-sex education and ties to Catholicism had to go. As she told Mr. Kenney: “It became clear to me that it was change or go out of business, and what the change had to be was making the college available to a larger pool of students — Catholic, Protestant, Jewish, male, female. It was change or die.”

In stages, Ms. McCormack transformed an elite, traditionally Catholic women’s school into a nonsectarian coeducational college with a new name, progressive curriculums and a more racially, ethnically and religiously diverse student body and faculty.

“I did some very difficult things, which were important for the future of the college,” Ms. McCormack said in an interview for this obituary in 2017. “I received praise and blame. But I believe one has to make difficult decisions and stick to them.”

Dismantling the school’s Catholic identity meant dropping the Sacred Heart name and cherished symbols of Christianity, including hundreds of crucifixes. Ms. McCormack and three young nuns gathered them up from all over the campus and, with groundskeepers’ shovels, buried them in the woods behind a playing field.

They did it on a Good Friday, the commemoration of the burial of Christ. “We thought it was an appropriate day,” she told Mr. Kenney.

She introduced curriculum changes over four years, eliminating grades and course requirements for graduation in favor of a “portfolio system,” with students charting their own courses of study and keeping portfolios of their work and extracurricular activities. A faculty board judged their achievements for graduation.

There were painful adjustments. In 1969, Black students occupied a classroom building, accusing the college of tolerating racism. Ms. McCormack did not call the police, but in five days of talks with protesters, she insisted that racial justice and the rights of the college community were valid causes. She made no definitive promises, and the protesters left peacefully after a week.

Manhattanville began admitting men in the 1971-72 academic year. A dormitory became coed, and curfews were dropped. By the end of her tenure, enrollment, 935 students when she started, had more than doubled, to 2,000, and government grants and private endowments were starting to roll in.

Over the years there were fusillades of protest from parents, alumnae and traditional Catholics, and once a bomb threat. Ms. McCormack said she received a picture of a stained-glass window depicting Judas kissing Jesus.

“This is you, Sister,” an anonymous alumna wrote.

“My thought was, ‘We certainly didn’t teach you Christian charity,’” Ms. McCormack told The Times.

But, Mr. Kenney wrote, “many of her accomplishments drew little controversy and set her mark upon the institution for many years to come.” He added, “The changes Elizabeth made almost certainly saved the college from closing.”

Even before stepping down as Manhattanville’s president, she had begun to question Catholic teachings on celibacy, birth control, divorce, homosexuality and abortion. She also questioned her own vocation. In 1974, she was released from her vows.

By then, she said, she was in love with Jerome Aron, whom she had hired as the college’s chief financial officer in 1969. After his divorce, they were married in 1976 by a rabbi, and then in 1978 in a Catholic ceremony. Mr. Aron died in 2004.

In addition to Nicholas Arons, her grandson, Ms. McCormack is survived by four of Jerome Aron’s children, Nan, Peter, Betsy and Mark Aron; six other grandchildren; and five great-grandchildren.

Elizabeth Jane McCormack was born in Manhattan on March 7, 1922, one of two children of George and Natalie (Duffy) McCormack. Her father was the president of an architectural firm. In 1926, the family moved to Larchmont, N.Y.

She attended St. Augustine’s Academy in Larchmont, and in 1940 she graduated from Maplehurst, a Catholic girls’ boarding school in the Bronx. She read voraciously, especially the Romantic poets Shelley, Keats and Coleridge.

Ms. McCormack attended Mass daily at Manhattanville and was in her senior year when she decided to become a nun. She took her final vows in Rome in 1952. After four years as headmistress of a Catholic high school in Greenwich, Conn., she earned a master’s degree at Providence College in Rhode Island and a doctorate at Fordham University in the Bronx. She joined the Manhattanville staff in 1958 and was a dean and administrator before becoming president.

Ms. McCormack became a philanthropic adviser to the Rockefeller family in 1974. She had little money, and a Rockefeller lawyer asked about that.

“She pulled out past checks that she had received as salary for being the college president — seven years’ worth of checks, and every one — one after the other — was signed over to the Society of the Sacred Heart,” Mr. Kenney recalled. “She had never cashed her paychecks.”

She began advising 22 Rockefeller cousins, the great-grandchildren of the patriarch, John D. Rockefeller. Their interests were scattered. But her personalized guidance focused on conservation, health, education, the arts and other beneficiaries.

Ms. McCormack, who lived in Manhattan, became a trustee of the Population Council, chairwoman of the MacArthur Foundation and a director of the Atlantic Philanthropies, Memorial Sloan Kettering Cancer Center and dozens of other foundations, corporations and colleges.

“To use your money to make a difference is something one has to learn,” Ms. McCormack wrote in a 2004 article for The Chronicle of Philanthropy. “You have to think broadly, and in my opinion, give narrowly.”

Natalie Prieb contributed reporting.

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