Dylann Roof is alleged to have walked into the building and opened fire in June 2015 in an attempt to start a race war.
Judge Richard Gergel said jury selection at the court in Charleston will start on Monday. The jury will first decide on a verdict and then, if Roof is guilty, whether he should face the death penalty.
He faces state charges including nine murder counts at Emanuel African Methodist Episcopal Church.
He also faces federal charges including hate crimes and obstruction of the practice of religion.
US attorney general Loretta Lynch has said federal charges were necessary to adequately address a motive that prosecutors believe was unquestionably rooted in racial hate. South Carolina has no state hate crimes law.
Roof is white and allegedly wrote online of committing racial violence, and federal authorities have said he used a personal manuscript in which he decried integration and used racial slurs to refer to black people.
A federal indictment says Roof planned for months to increase racial tensions throughout the country and seek retribution for perceived wrongs he thought had been committed against white people.
No time frame has been put on the trial.
