The order, which Trump inked during a ceremony in the White House Rose Garden, directs the IRS not to take "adverse action" against churches and other tax-exempt religious organizations participating in political activity that stops short of an endorsement of a candidate for office.
But pastors are already free to deliver political speeches, and regularly do. Churches and other tax-exempt organizations are restricted from endorsing or explicitly opposing political candidates under the 1954 Johnson Amendment, but the executive order Trump signed Thursday makes clear that those activities would still not be permitted.
Instead, the order prevents the IRS from expanding its restrictions on political activity by religious groups. It 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.
Evangelical Christian leader Russell Moore said the order is "more symbolic than substantive."
"The very fact that religious freedom is part of the conversation and religious freedom is being affirmed I think is a step in the right direction," he said on CNN's "Erin Burnett OutFront" Thursday night. "Now obviously if this is the end of the story, I'm really disappointed, but I think we ought to hold out the hope that this is just the beginning and that there are more steps to be made."
During remarks Thursday, Trump said the order would prevent religious groups from being singled out for their political views.
"We will not allow people of faith to be targeted, bullied or silenced anymore," Trump proclaimed, which were marking the National Day of Prayer. "And we will never, ever stand for religious discrimination. Never, ever."
Trump's language stood in contrast to certain steps his administration has taken to bar entry to citizens from some Muslim-majority nations and his campaign trail vows to stop all Muslims from entering the country. Courts have put his travel ban executive orders on hold -- finding Trump's own words provided evidence of a "Muslim ban."
Religious discrimination is barred by the US Constitution.
In his remarks, Trump said that "pastors, priests and imams" were targeted by the Johnson amendment, and would be freer to engage in political activity under his executive order.
The 1954 Johnson amendment says any tax-exempt group can lose its exemption if it is found to have endorsed or actively opposed a candidate for political office. The IRS is officially tasked with investigating suspected violators of the law, though only one organization has lost its exemption as a result of IRS action in the six decades the law has been in place.
Legal experts said the order would not have a discernible effect on policy.
"President Trump's executive order did not ease the current restrictions on political activity by religious organizations," said Lawrence Noble, general counsel of the Campaign Legal Center. "The executive order allows the IRS to restrict the activity it currently considers political, but prohibits the IRS from expanding the restrictions to cover activity not covered before the executive order."
The order, which declares that it is the policy of the Trump administration "to protect and vigorously promote religious liberty," also stops short of offering broad exceptions for groups to deny services based on religious grounds.
An earlier version of the order, which had previously leaked to The Nation, would have provided sweeping legal protections for people to claim religious exemptions, provisions that civil liberties groups claimed would allow for discrimination against LGBT Americans.
"America has a rich tradition of social change beginning in our pews and our pulpits," Trump said in front of an audience of religious leaders Thursday. "We must never infringe on the noble tradition of change from the church and progress from the pew."
"Under my administration, free speech does not end at the steps of a cathedral or a synagogue or any other house of worship," he went on. "We are giving our churches their voices back and we are giving them back in the highest form."
Trump himself vowed early in his presidential tenure to get rid of the measure, though completely striking the amendment would require an act of Congress.
"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," Trump said in February.
Some religious leaders, however, object to any measure that would make it easier to inject politics into places of worship.
"For decades, the Johnson amendment has prevented houses of worship from being turned into partisan political tools. A majority of clergy -- and Americans -- support the status quo and oppose political endorsements from the pulpit," Interfaith Alliance president Rabbi Jack Moline said. "President Trump's executive order reportedly aims to gut the Johnson Amendment and clear the way for the Religious Right to weaponize their churches for partisan battle."
"If the effort succeeds these churches would become conduits for unregulated 'dark money' in elections, with no restrictions or disclosure requirements," he said.
In a letter delivered to House and Senate leaders last month, a group of religious leaders argued against scrapping the Johnson amendment, citing similar concerns that such a move could turn religious groups into political organizations.
"The charitable sector, particularly houses of worship, should not become another cog in a political machine or another loophole in campaign finance laws," the group wrote.
Briefing reporters Wednesday evening, a senior Trump administration official downplayed the possibility that churches would soon act as political groups advocating for particular candidates.
"Nobody is suggesting that churches are allowed, or it's legal, for tax-exempt organizations to tax out ads endorsing candidates," the official said. "That's illegal now for them, as a condition of their tax-exempt status. So we're not changing what's legal, we're not changing what's illegal, just enforcement discretion."
Selectively enforcing law has drawn scrutiny in past administrations, and before the order was signed Wednesday, some experts predicted it could present another legal challenge to Trump's administration.
The American Civil Liberties Union threatened the Trump administration with a lawsuit when details of the executive order emerged Wednesday.
But on Thursday, the group rescinded its threat, saying the order had no teeth.
"It turned out the order signing was an elaborate photo-op with no discernible policy outcome," the organization tweeted. "Trump's assertion that he wished to 'totally destroy' the Johnson amendment with this order has proven to be a textbook case of 'fake news.'"
CNN's Elizabeth Landers, Jeremy Diamond and Leigh Munsil contributed to this report.