ABC13 was there as a handcuffed Andre Jackson was walked out into the hallway and said what sounded like, "I'm Grace Jones' son," appearing to reference the supermodel. It's not clear why he made the claim.
His bond was set at $500,000.
WATCH: Andre Jackson at court
Jackson was originally arrested and charged on June 3, 2016 in the boy's stabbing death, but the charges were dropped.
He now faces a new murder charge after Houston police arrested him without incident Tuesday morning in Baytown during a traffic stop.
ABC13 Eyewitness News learned the break in this case came when local investigators sent some of the DNA collected to DNA Labs International, a private company based in Florida.
The company would not disclose how they were able to get the DNA match tying Jackson to Josue's murder.
Josue was stabbed to death while walking home from Marshall Middle School on May 17, 2016 in north Houston.
Witnesses said in his last moments, Josue could be heard screaming, "Don't kill me, please!"
A friend of the Flores family was in court Wednesday to show that the whole Northside community is standing with Josue.
"It's our turn to be his voice. It's our turn to support him, the family, and justice. We hope that justice prevails no matter what the situation is," Miguel Chavez said.
Members of the @houstonpolice department have taken the suspect into custody without incident. We are proud of the steadfast work of our women & men and our partners @FBIHouston, and all who played a role in getting us to this point. Our thoughts are with the Flores family. https://t.co/qdDgbeYBd0— Chief Art Acevedo (@ArtAcevedo) June 18, 2019
"We were able to make a case to the grand jury that Jackson is in fact the murderer of Josue Flores," said Harris County District Attorney Kim Ogg.
On the three-year anniversary of Josue's death, Houston Police Chief Art Acevedo and cold case detectives reiterated that Jackson is still a person of interest in the case.
After Acevedo's comments, Jackson claimed his innocence in a 10-minute YouTube video.
"I am innocent and need the public to understand institutionalized racism and systematic prejudice, which will be the topic of a book that I am publishing," Jackson said at the time.
Jackson also claimed he was being "harassed."
"I have nothing to do with this case. You can stop considering me a suspect. You can stop mentioning my name in this case," Jackson added.
Last Friday, ABC13 Eyewitness News was the first to report that investigators discovered new physical evidence in the murder case.
Now Jackson has been charged. Police said they had him under 24/7 surveillance for several days.
Ogg said that though she is not allowed by law to discuss the specifics of the grand jury proceedings, she pointed again to the newly-tested evidence.
"I am willing to stand with these prosecutors that it is evidence beyond a reasonable doubt of Andre Jackson's guilt," Ogg told the media.
Houston Mayor Sylvester Turner said that he and Acevedo met with Josue's family last week about the developments.
"The sixth grader was a smart, loving and respectful student. His family misses him dearly every day, the community misses him," Turner said of Josue.
"For the past three years, our department has worked tirelessly to bring justice to Josue, the Flores family, and our extended community," Acevedo said in a statement. "Today's true bill is a significant step in our journey to justice, and we look forward to supporting the Flores family as this case proceeds through the criminal courts."
The news of the arrest Tuesday was a long time coming for Flores' family and neighbors.
Some of them started crying as Jackson's arrest was announced.
"We were just waiting. Waiting, waiting, waiting and this day has finally gotten here. I'm just so happy," said Stella Mireles-Walters.
Mireles-Walters is the organizer of "Safe Walk Home Northside," the group that was started after Josue was murdered walking home from school.
BREAKING: New charges announced in the murder of 11-year-old Josue Flores!! The man who was arrested and later released has been charged AGAIN.— Katherine Marchand (@KatherineMABC13) June 18, 2019
Neighbors are watching the announcement with tears in their eyes. https://t.co/XHdCxmvAK7 pic.twitter.com/cG3wzXK08N
"I just ask you to put yourself in that mother's position, three years waiting for justice. No one is going to rush, and nobody is going to say anything to jeopardize that because the ultimate justice is when he's locked up in prison, and that's what I want us to focus on today," said HPD Executive Assistant Chief Troy Finner.
Timeline of the Josue Flores murder case
Josue Flores stabbed 20 times: investigators
'Stop mentioning my name': Person of interest in Josue Flores' murder claims his innocence on YouTube
Houston police renew effort to find Josue Flores' killer
Police: 11-year-old boy fatally stabbed in north Houston
U.S. Marshals arrest man accused of fatally stabbing boy walking home from school in north Houston
Man falsely accused in boy's stabbing hopes police find Josue Flores' real killer
Mayor Turner makes plea for information in boy's stabbing death
HPD releases image of person of interest in Josue Flores case