When Pope Francis was elected in March 2013, American nuns who belong to the Leadership Conference of Women Religious (LCWR) were optimistic that they would enjoy a fresh start. The group, which represents 80 percent of American nuns, had been lambasted under Pope Benedict XVI for “pushing radical feminist themes incompatible with the Catholic faith.”

Since Francis seemed to be the polar opposite, they had every reason to hope the clampdown would be lifted. After all, in his first six months in office, he managed to tighten the reins on extravagant priests and even seemed to bend on gays in the priesthood. Why not lighten up on the nuns, too?

But the sisters, it seems, were dead wrong to think they might get a fair shake under Francis. In what is being viewed as an even stronger clampdown, the Vatican has essentially warned the nuns that they must reform their organization and mend their errant ways or risk further scrutiny by the Holy See. In scathing remarks at an April 30 meeting, Cardinal Gerhard Müller, the prefect for the Congregation for the Doctrine of the Faith, criticized the nuns’ choice of speakers to address their conferences, their leadership awardees, and the lack of spiritual guidance in their work.

And lest anyone assume the strong language was a leftover from Benedict’s days, Müller made sure the nuns knew Francis heartily endorsed the criticism. “What the Holy Father proposes is a vision of religious life and particularly of the role of conferences of major superiors which in many ways is a positive articulation of issues which come across as concerns in the doctrinal assessment,” he said. “I urge you to reread the Holy Father’s remarks and to make them a point of discussion with members of your board as well.”

What Müller was specifically referring to, among other things, was the LCWR’s choice to honor Sister Elizabeth Johnson with its most prestigious leadership award. A prominent theologian from Fordham University, Johnson has been a thorn in the side of the United States Conference of Catholic Bishops, which has criticized her work, including her popular book Quest for the Living God: Mapping the Frontiers in the Theology of God. “It saddens me to learn that you have decided to give the Outstanding Leadership Award during this year’s assembly to a theologian criticized by the bishops of the United States because of the gravity of the doctrinal errors in that theologian’s writings,” Müller told the LCWR. “This is a decision that will be seen as a rather open provocation against the Holy See and the doctrinal assessment. Not only that, but it further alienates the LCWR from the bishops, as well.”

Muller then went on to inform the LCWR that it will be required to get approval from Seattle Archbishop J. Peter Sartain, whom Benedict assigned to guide the group through reforms, for almost everything it does that concerns the public. Sartain, he said, would be far more involved in the group’s decisions and daily business from now on. Müller warned the sisters to pay special attention to the LCWR’s annual assembly in August, when new speakers and awardees will be named. “I also understand that plans for this year’s assembly are already at a very advanced stage, and I do not see the need to interrupt them,” he said. “However, following the August assembly, it will be the expectation of the Holy See that Archbishop Sartain have an active role in the discussion about invited speakers and honorees. “

The LCWR is choosing not to give interviews on the meeting, but it did confirm to the National Catholic Reporter that Müller’s meeting notes were accurate in terms of tone and tenor. In a statement posted on their website, the sisters said, “As articulated in the Cardinal’s statement, these remarks were meant to set a context for the discussion that followed. The actual interaction with Cardinal Müller and his staff was an experience of dialogue that was respectful and engaging.”

In an interview with The Daily Beast before Francis’s election, then LCWR president Sister Florence Deacon said she had high hopes for the new pope. “It is important that we have a leader who appreciates the roles of the laity and of women religious who have accepted its call to renewal and who are committed to building a more just and peaceful world,” she said.

The clampdown on the nuns began in 2012, when the Congregation for the Doctrine of the Faith issued its original doctrinal assessment after investigating the organization. Then it chastised the sisters for staying silent on some of the church’s signature issues, including birth control, euthanasia, homosexuality, and the ordination of women. Instead, in their work in schools, hospitals, and centers for the poor, they were just doing what they could to help the population, rather than acting as missionaries for the church. Their silence on the issues was interpreted as an endorsement, which was particularly annoying to the United States Conference of Catholic Bishops, which felt the sisters were undermining the status quo.

According to the doctrinal assessment of the LCWR, the sisters were “moving beyond the Church” and as such, creating “a serious source of scandal” that is incompatible with religious life.

The nuns’ next trial of faith will be their August assembly, which will be seen as a litmus test for just how seriously they are taking the Vatican’s criticism. Their options will be to get in line with with the bishops and cardinals or break away and form their own group outside the Holy See’s jurisdiction.

Francis, for his part, does not appear flexible on the topic. In several interviews, including one last September with the Jesuit magazine America, he dismissed the idea of women as equals. “I am wary of a solution that can be reduced to a kind of ‘female machismo,’ because a woman has a different make-up than a man. But what I hear about the role of women is often inspired by an ideology of machismo,” he said then. Now it is up to the nuns to flex their muscles or succumb.