COLUMBIA, S.C. — Joey Meek, a friend of admitted Charleston shooter Dylann Roof, on Friday pleaded not guilty to two charges related to the June massacre that left nine people dead at a historic black church.

Meek, 21, was charged by a federal grand jury with one count of making false statements to federal officials and one count of “misprision of a felony,” meaning he concealed knowledge about a crime. U.S. Magistrate Judge Shiva V. Hodges said during a hearing here that the only plea she could accept was one of not guilty; that plea was entered on Meek’s behalf.

Meek “is alleged to have taken steps to conceal his knowledge of the crimes committed by Dylann Storm Roof,” according to the Justice Department, “and to have made materially false statements when Meek told a special agent of the FBI that he did not know specifics of Roof’s plan to shoot individuals on a Wednesday, during Bible study, at an [Emanuel] AME Church in Charleston.”

Kim Konzny, Meek’s mother, burst into tears Friday at the sight of her son clad in an orange jumpsuit, shackled at the hands and feet. “We love you,” she whispered as her son rocked back and forth.

As Meek exited the courtroom, his father asked: “Do you need canteen money?”

Meek was arrested Thursday by FBI agents. He may be released on a $100,000 secured bond, though it is unclear whether his family will be able post the bond to secure his release. His attorney, Deborah Butcher, told the judge that Meek’s entire family is in the Columbia area and he is “not a flight risk.”

Butcher declined to comment outside the courthouse. Meek’s family also declined to comment before and after the hearing.

In the weeks before Roof allegedly gunned down nine worshipers inside the historic black church, he slept on the floor of a Lexington County, S.C., trailer that also housed Meek. Meek’s two brothers, mother, and girlfriend also live in the trailer; The Washington Post profiled the family on Sunday.

Meek told The Post that when news broke about the shooting, he feared Roof was the suspect; he said he called police once he saw surveillance footage of the suspected shooter on television the next morning. Meek said FBI agents subsequently questioned him about what Roof had told him before the church massacre, as well as his own possible involvement in the shooting.

His girlfriend, Lindsey Fry — who said she was also questioned — told The Post that Meek was taken into custody at work Thursday afternoon.

“He don’t think he did anything wrong,” Fry said in a phone interview. “I don’t really have anything to say about it.”

“I mean, we knew it was going to happen,” she said of the arrest, “but we don’t understand why it was happening.”

Fry declined to comment at the courthouse Friday.

Meek has said he and Roof were childhood friends and that Roof had asked him for a place to stay. In the days before the shooting, Meek said Roof told him he was going to “do something crazy,” so Meek and Fry hid Roof’s gun. They later returned it, believing the statement was nothing more than a drunken rant.

“I didn’t take him seriously,” Meek said.

During the hearing Friday, Shiver read the indictment against Meek and had him sign a copy. On the first charge, misprision of a felony, Meek could face a maximum of three years in prison and a $250,000 fine. On the second, making a false statement to a federal agent, he could face a maximum five-year sentence with a $250,000 fine. Both charges also carry a year or more of supervised release.

The judge noted that Meek is currently on probation. His attorney, Butcher, outlined Meek’s life: He has a 10th-grade education, she said, went through ROTC and and lives with his mother.

On previous charges, Butcher said, Meek had “always shown up for court. He will be where he needs to be when required. He does not come from a family of means.”

A prosecutor said Meek “refused to appoint counsel” after receiving a letter in August from the U.S. Attorney’s Office, informing him that he was under investigation. The prosecutor also noted that Meek has a criminal record.

In December 2011, when Meek was just 17, he and an accomplice broke into a nearby home and stole electronics and jewelry, according to an arrest warrant. He was later caught when he tried to sell an iPod at a GameStop store and showed the clerk his ID. The burglary charge in that case was dropped as part of a plea deal after Meek pleaded guilty to playing a role in stealing a car a few months later, in January 2012, according to court papers.

He and a juvenile accomplice, according to an arrest warrant, drove to a Wal Mart and stole a 2009 Ford Flex from the parking lot. The pair was identified by surveillance footage.

At the hearing in federal court Friday, Butcher said Meek did send her a copy of the August letter from the U.S. Attorney’s Office, but that “he was unsure what the letter was. I was not sure what the letter was. He wasn’t trying evade law enforcement.

Addressing Meek, the judge obliquely referred to his prominence in the press, saying that if he divulged conversations between himself and his attorney, they would no longer be privileged and could be used against him. She also instructed him not to talk to any victims or witnesses in the Roof case.

“These charges against you are serious,” she said.

Meek wiped his eyes after he sat down. Looking at his family and girlfriend, he appeared to mouth, “I’m not going to get out,” before being led out of the courtroom.

Butcher may not stay on the case. Hodges, the judge, tentatively set another hearing for Wednesday to ensure Meek has appropriate representation. Meek has signed an affidavit affirming that he can not afford to hire a lawyer.

Roof faces nine counts of murder and three counts of attempted murder in the June 17 shooting spree. A South Carolina judge set a July 11, 2016, trial date for Roof.

CORRECTION: A previous version of this story incorrectly identified the mother of Joey Meek. The post has been updated. Bever and Izadi reported from Washington. Adam Goldman, Stephanie McCrummen, Sarah Larimer and Abby Phillip contributed to this story, which has been updated.