Dylann Roof was transferred Friday afternoon from the Charleston County jail where he has stayed since his arrest in the Emanuel AME Church massacre.
The U.S. Marshals Service took custody of the convicted killer about 1:15 p.m., jail records and Lt. Rita Zelinsky of the Charleston County Sheriff's Office confirmed.
The move came 11 days after Roof, 23, pleaded guilty to state murder charges in the 2015 shooting, effectively wrapping up local court proceedings in his prosecution.
He had already been convicted on 33 federal charges, including hate crimes, and sentenced to death in a separate proceeding earlier this year.
The self-avowed white supremacist from Eastover sat through most of a Bible study at the Calhoun Street church on June 17, 2015, before killing nine black parishioners in an apparent bid to start a race war.
It was unclear where Roof would go after his transfer from the Sheriff Al Cannon Detention Center.
Weeks ago, the state ceded formal custody of Roof to federal authorities, clearing the way for him to spend time in a federal facility while awaiting execution.
Until his transfer Friday, he had remained at the county jail.
Eventually, he will be taken to a U.S. Bureau of Prisons facility, though agency records showed he was not immediately in its custody Friday afternoon. His assigned prison will not be made public until he arrives there, agency spokeswoman Tovia Knight said.
South Carolina has medium-security federal prisons in Estill and Edgefield. A prison in Terre Haute, Ind., houses death row inmates.