Dylann Roof ignored his legal team's advice and asked the judge if he could represent himself.
The 22 year old's alleged to have sat through an hour of Bible study at the black majority church in Charleston before opening fire in June 2015.
In court Roof asked US District Judge Richard Gergel if he could represent himself. The judge replied that he would reluctantly accept the "unwise" decision.
High profile attorney David Bruck then slid over and let Roof take the lead chair in court. The lawyers can stand by and help Roof if he asks.
Federal prosecutors are seeking the death penalty against Roof on hate crime, obstruction of religion and other charges.
On Monday 516 potential jurors reported to the courthouse to be individually questioned by the judge.
A process will the begin to choose 12 jurors and six alternates before the trial begins.
Jurors will first decide if Roof is guilty and then if he should face the death penalty.
The judge has already decided that Roof is fit to stand trial after the defence raised questions about his mental health.
