"I would like to express my esteem and gratitude to the religious women of the United States," the Pope said to applause that resonated through the city's stately St. Patrick's Cathedral. "What would the Church be without you?"

Speaking during evening prayers Thursday at St. Patrick's Cathedral, Francis continued:

"Women of strength, fighters, with that spirit of courage which puts you on the front lines in the proclamation of the Gospel. To you, religious women, sisters and mothers of this people, I wish to say 'thank you,' a big thank you... and to tell you that I love you very much."

Nuns await the arrival of Pope Francis in St. Patrick's Cathedral.

The Pope's high praise came just months after the Vatican wrapped up a controversial investigation of an umbrella group of American nuns.

In 2012, the Vatican accused the Leadership Conference of Women Religious, the country's largest group of Catholic nuns, of sponsoring "certain radical feminist themes incompatible with the Catholic faith." American bishops were appointed to oversee the LCWR and the speakers invited to their conferences. That oversight abruptly ended in April.

A separate Vatican investigation encompassed all American "women religious" -- as Catholic sisters and nuns are officially known -- and sought to understand why their membership has dropped so deeply for decades. That investigation ended without any censure of the Catholic women, but some said they were deeply offended by its premise.

Pope Francis speaks during vespers Thursday night.

Francis has previously said that women in the church are "more important than bishops and priests." In December of last year, he told a gathering of female theologians they were "strawberries on the cake."

Costello: Pope Francis, women are waiting

Francis has been working to elevate the role of women without changing church doctrine that bars them from the priesthood.

He has appointed women to a few powerful Vatican positions, including the committee to combat sex abuse in the Catholic Church. Roughly half of that 17-member committee is made up of women.

According to Vatican Radio, just 18% of the Vatican's workforce overall is female, including employees at Vatican museums, post offices and the Holy See that governs the Roman Catholic Church.

In his message on Thursday, Francis also called attention to the pain recent scandals in the church have caused.

"You suffered greatly in the not distant past by having to bear the shame of some of your brothers who harmed and scandalized the Church in the most vulnerable of her members," Francis said, referring to the clergy sex abuse scandal that harmed thousands of children, demoralized many Catholics and cost the church more than $1 billion in legal settlements.

In the main, the Pope's message was a pep talk to his audience of priests and nuns. He told them he is with them in this time of "pain and difficulty" and thankful for their faithful service.

The Pope acknowledged the challenges they face "adapting to an evolving pastoral landscape."

Francis began the service by offering prayers after the tragedy at Mecca, expressing "my sentiments of closeness," to the hundreds of Muslim pilgrims who lost their lives in Saudi Arabia. A stampede during one of the last rituals of the Hajj season -- the annual Islamic pilgrimage to Mecca -- killed more than 700 people and injured close to 900.

"In this moment I give them assurances of my prayers," Francis said.

Francis' visit to St. Patrick's Cathedral marked the fifth pontifical trip to the site. More than five million people walk through the church's iconic bronze doors each year.

Francis said the cathedral can serve as a "symbol of the work of generations of American priests and religious, and lay faithful who helped build up the Church in the United States."

The cathedral, which opened in 1879, is the seat of the Archbishop. It has been through an extensive renovation estimated at $175 million.

Francis' evening prayers capped a busy day. Thursday morning, he addressed Congress in a speech that focused on immigration, the death penalty, racial injustice, the weapons trade, and poverty. Friday, he'll address the United Nations.

This weekend, the Pope will go to Philadelphia for the World Meeting of Families, a large Catholic event that is expected to draw nearly 1 million pilgrims to papal Masses.