The order, signed during a ceremony in the White House Rose Garden, directs the Internal Revenue Service to exercise "maximum enforcement discretion" over the so-called Johnson amendment, which prevents churches and other tax-exempt religious organizations from endorsing or opposing political candidates. The order also provides "regulatory relief" for organizations that object on religious grounds to a provision in Obamacare that mandates employers provide certain health services, including coverage for contraception.
A message left with the White House asking what assurances the administration could offer LGBT Americans anxious over the order was not immediately returned Thursday.
But the head of the Congressional LGBT Equality Caucus, a group consisting of gay lawmakers and their allies, worries that the administration will use the order to harm gay Americans.
"The LGBT Equality Caucus will remain vigilant for any attempt to undermine the hard-fought gains our community has made in the past decade," Executive Director Roddy Flynn told CNN Thursday. "We plan on closely monitoring the implementation and interpretation of the executive order."
"This administration has attacked the rights of transgender students and programs assisting LGBT elders," he added. "We cannot trust that this order will be narrowly utilized to not directly harm our community. We will be watching."
Other leaders claimed the order will allow Attorney General Jeff Sessions to use the Justice Department to discriminate against LGBT Americans.
"Donald Trump just let the fox into the henhouse," said Sarah Warbelow, legal director of the Human Rights Campaign, one of the country's most influential LGBT rights groups. "Through this executive order, Trump has directed Attorney General Jeff Sessions -- a man who has denied LGBTQ people equality under the law -- to seek a license to discriminate across all areas of the government."
"We are watching and we will challenge any effort by Jeff Sessions or other agencies of Trump's administration to license discrimination," she added.
The leadership of PFLAG National, an LGBT organization for families, said the lives of gay Americans could be controlled by other people's ideologies under Trump's new order.
"In signing this so-called 'religious liberty' order, the president has essentially granted broad permission to discriminate, and ceded enormous power to unelected officials to interpret regulation and current law," Interim Executive Director Elizabeth Kohm told CNN. "We are deeply concerned that rights and protections for people from marginalized communities will be even further subject to the whims of others' personal ideology controlling their lives, a concept entirely antithetical to the values of freedom and dignity our nation holds dear."
Sarah Kate Ellis, president and CEO of GLAAD, an LGBT media organization, said the President's executive order is a "slippery slope" toward discrimination.
"Today's Executive Order stopped short of rampant discrimination but don't be fooled this begins a slippery slope of a #LicenseToDiscriminate," she tweeted Thursday.
But the head of Log Cabin Republicans, a group that represents gay conservatives, said the idea that the executive order harms gay Americans is "total nonsense."
"Once again, stories about a Trump 'anti-LGBT executive order' were total nonsense," Gregory T. Angelo told CNN. "Not only is the text of the executive order completely agnostic on LGBT-related matters, the Trump administration has now explicitly asserted that there were not plans for a separate order that addressed LGBT issues."