When President Donald Trump issued a flurry of executive orders during his first weeks in office, his mixed message on religious freedom rightly stirred questions and criticism from Catholics.

On the one hand, during an address at the National Prayer Breakfast, Trump repeated his campaign pledge to repeal the Johnson Amendment, which bars churches and other tax-exempt groups from endorsing political candidates from the pulpit and raising funds for their campaigns.

However, the new president also backed a 2014 executive order issued by President Barack Obama that prohibits discrimination based on sexual orientation by federal contractors, with no exemptions for church-affiliated institutions.

President Trump is “proud” to have been the first Republican presidential nominee “to mention the LGBTQ community in his nomination acceptance speech, pledging then to protect the community from violence and oppression,” read the Jan. 31 White House statement that confirmed his plan to leave the executive order in place.

Meanwhile, after a separate draft executive order that proposed broad religious-freedom protections in federal programs sparked headlines claiming it “could allow a denial of service to gays,” the document was shelved, at least for the present.

The outcome disappointed religious-freedom advocates, who were already concerned about the impact of other executive orders that restricted the flow of refugees into the country and could make it tough for persecuted religious minorities from the Middle East to enter the U.S.

The U.S. bishops quickly pressed the administration to clarify its message on religious freedom. “In seeking to remedy instances of discrimination, [the executive order] creates new forms of discrimination against people of faith,” read a Feb. 1 statement released by the U.S. Conference of Catholic Bishops, which expressed the hope that conscience protections would still be inserted into the document.

Issued by the Obama administration in 2014, the order prohibits federal contractors from workplace discrimination based on sexual orientation and gender identity. When the document was released, the bishops warned,

“With the stroke of a pen, it lends the economic power of the federal government to a deeply flawed understanding of human sexuality, to which faithful Catholics and many other people of faith will not assent.”

While most state laws that provide similar protections have featured a religious exemption, Obama’s order failed to provide this provision. Thus the bishops feared that Catholic nonprofits that refused to offer benefits to same-sex partners, or allow employees to choose the bathroom that corresponded with their chosen gender identity, could be disqualified from participation in federal programs.

Ryan Anderson, the co-author of Debating Religious Liberty and Discrimination, a new book that will be out in April, told the Register that Trump should both rescind Obama’s executive order and issue the draft executive order on religious freedom that was leaked to the media.

Entitled “Establishing a Government-Wide Initiative to Respect Religious Freedom,” the draft document “protects the religious liberty rights of all Americans in very tailored ways that address the problems of today,” Anderson told the Register.

If signed by Trump, the draft executive order would effectively resolve the legal challenges against the HHS mandate filed by religious nonprofits, like the Little Sisters of the Poor and the Register’s parent company, EWTN.

Further, it would protect “religious organizations’ right to maintain their mission and identity in their staffing decisions and programming, while not losing the ability to partner with the government,” he said.

It is not entirely clear why Trump opted to endorse Obama’s executive order. But it is worth noting that his populist message never featured sweeping protections for Americans who objected to the latest sexual orthodoxies on religious grounds.

In contrast, Trump has fulfilled his promise to take steps to repeal the Johnson Amendment, a key priority for some evangelical pastors who endorsed his nomination amid ongoing questions about his character and weak record on life and religious-freedom issues.

“I will get rid of and totally destroy the Johnson Amendment and allow our representatives of faith to speak freely and without fear of retribution,” he said during his address at the National Prayer Breakfast.

The U.S. bishops have not issued a formal response to this initiative, possibly signaling their own policy priorities.

“Religious organizations should be able to engage in ordinary religious speech that deals with politics,” said Anderson, when asked to interpret the bishops’ stance on the Johnson Amendment. But other challenges “pose more of a threat to the mission and identity, and in some cases even existence, of religious organizations,” he said. At issue is a religious institution’s ability to “retain nonprofit tax status, accreditation, licensing and eligibility for government programs without passing a government-imposed orthodoxy on matters of human sexuality, for example.”

At the National Prayer Breakfast, Trump embraced religious freedom as “a sacred right” that is “under threat all around us.” But his actions ignore the full scope and promise of the “first freedom.”

Now it will be up to Catholics to make their voices heard, inspired by the Church’s own teachings on religious liberty. This right, states the Catechism of the Catholic Church, is “based on the very nature of the human person, whose dignity enables him freely to assent to the divine truth which transcends the temporal order” (2106).

Genuine freedom of religion cannot be restricted to the four walls of a church or even to political engagement. It’s time to challenge the logic of government regulations that seek to affirm the rights of one group, only to restrict the rights of other citizens who rightly ask for the freedom to serve according to their own beliefs.