Lemon, now an independent journalist, livestreamed a protest against Trump's deployment of thousands of armed immigration agents into Democratic-governed Minnesota's biggest cities.
The protest disrupted a January 18 service at Cities Church in St Paul.
A magistrate judge on Friday ordered Lemon released to await trial, after a night in custody following his arrest late on Thursday by the FBI.
Dressed in a cream-coloured double-breasted suit, Lemon spoke only to say "yes, your honor" when asked if he understood the proceedings. One of his lawyers said that he pleaded not guilty.
"He is committed to fighting this. He's not going anywhere," said Lemon's lawyer Marilyn Bednarski.
"I have spent my entire career covering the news. I will not stop now," Lemon told reporters after the hearing.
"I will not be silenced. I look forward to my day in court."
A grand jury indictment charged Lemon with conspiring to deprive others of their civil rights and violating a law that has been used to crack down on demonstrations at abortion clinics but also forbids obstructing access to houses of worship.
Six other people who were at the protest, including another journalist, are facing the same charges.
Thousands of protesters took to the streets of Minneapolis and other US cities on Friday to denounce an immigration crackdown in which federal agents fatally shot two US citizens, sparking one of the most serious political crises Trump has faced.
Free press advocates voiced alarm over the arrests. Actor and activist Jane Fonda went to show support for Lemon, telling journalists the president was violating the Constitution.
"They arrested the wrong Don," Fonda said.
Trump, who has castigated the protesters in Minnesota, blamed the Cities Church protest on "agitators and insurrectionists" who he said wanted to intimidate Christian worshippers.
Organisers told Lemon they focused on the church because they believed a pastor there was also a senior US Immigration and Customs Enforcement employee.
More than a week ago, the government arrested three people it said organised the protests.
But the magistrate judge in St Paul who approved those arrests ruled that, without a grand jury indictment, there was not probable cause to issue arrest warrants for Lemon and several others the Justice Department also wanted to prosecute.
"This unprecedented attack on the First Amendment and transparent attempt to distract attention from the many crises facing this administration will not stand," Abbe Lowell, Lemon's lawyer, said in a statement, invoking constitutional free speech protections.
In the livestream archived on his YouTube channel, Lemon can be seen meeting with and interviewing the activists before they go to the church, and later chronicling the disruption inside, interviewing congregants, protesters and a pastor, who asks Lemon and the protesters to leave.
Independent local journalist Georgia Fort and two others who had been at the church were also arrested and charged with the same crimes.
US Magistrate Judge Dulce Foster on Friday ordered Fort's release, denying prosecutors' request to hold her in custody, according to court documents.
The Justice Department over the past year has tried to prosecute a succession of Trump's critics and perceived enemies.
Trump frequently lambastes journalists and news outlets, going further than his predecessors by sometimes suing them for damages or stripping them of access-granting credentials.
with AP
