"We will not allow people of faith to be targeted, bullied or silenced anymore," Trump said. "And we will never ever stand for religious discrimination. Never ever."
Hannah Simpson, 32, is a Jewish LGBT activist in both the conservative and reform movements. She said she began transitioning in 2012 and since the end of 2013, has been fully living as a woman.
Simpson told ABC News that she fears Trump's order giving religious organizations freedom to take a stand from the pulpit on political issues -- including LGBT rights and same-sex marriage -- could also lead to discrimination against people like her.
"It perpetuates further the perception that transgender people and those who are gender diverse are less worthy of civil protections and access to resources, even in the private sector, and less welcome in religious practices," Simpson said. "I think this is going to show itself in so many ways -- starting with things like access to or respect for one's identity and presentation in religious spaces."
Simpson said her own faith played a major role in her transition.
"I came to terms with myself and came into myself with God's help, not in spite of God," Simpson said. "I think it takes a tremendous amount of personal reflection and courage to take the most intricate machine on Earth -- the human body -- and say 'I need to make some edits, I need to mold this to my needs.'"
Simpson said she now attends services at an LGBT synagogue in New York City.
But while there are many religious organizations that have been supportive of trans people, others have engaged in discrimination, Susan Sommer, director of constitutional litigation at Lambda Legal, told ABC News.
"We absolutely do see discrimination by faith-based organizations against transgender people," Sommer said. "There's particularly troubling experiences that transgender people have at the hands of faith-based organizations that provide government-funded social services. They can use their religious beliefs to tell transgender people that there is something wrong with them."
"It seems like they're trying to set up a whack-a-mole situation where we don't know what the attorney general will be rolling out as guidance," Sommer said. "We have to remain extremely vigilant. We have been on high alert and will continue to be."
Coupled with the House of Representatives' vote on Trump's new health care bill later the same day, it was a "tough day for women," Kaylie Hanson Long, national communications director of NARAL Pro-Choice America, told ABC News.
"This executive order threatens our contraceptive benefits, which is of course so critical for women to be able to plan their own families and chart their own destinies," Long said.
Such curtailing of access to contraception impacts all women, but particularly those who are often marginalized, Long said.
But in a statement this evening, the American Civil Liberties Union said the order's wording was murky and questioned its actual effect, calling its signing "an elaborate photo-op with no discernible policy outcome."
“What President Trump did today was merely provide a faux sop to religious conservatives and kick the can down the road on religious exemptions on reproductive health care services," the statement continued.
However, the ACLU said that if this order "triggers" any action that infringes on "Americans’ right to exercise their religion and ensure their freedom from having others’ beliefs forced upon them," it stands "ready to sue the Trump administration ... again."
The organization had said earlier today that it was planning to sue over the order.
While the religious leaders present in the White House Rose Garden applauded as Trump signed the order, not all faith-based organizations are pleased. More than 90 organizations had previously sent a letter to congressional leaders opposing the measure, and others are speaking out.
Rev. Maria Swearingen and Rev. Sally Sarratt, a gay couple who lead Calvary Baptist Church in Washington, D.C., denounced the idea that churches should be endorsing and raising money for candidates.
"We have not and will not endorse political candidates from our pulpit," Swearingen and Sarratt told ABC News via email.
"If only more preachers concerned with changes to this amendment spent their time directly addressing the political and social needs of the most vulnerable among them and less time grasping after the power they think can be found in any one particular candidate, we might just have healthier, more authentic churches and a healthier, more engaged citizenry," they added.
ABC News' Lauren Pearle contributed to this report.