US District Judge Richard Gergel said 22-year-old Dylann Roof's wish to be his own lawyer was "unwise", but nevertheless granted his request.
The surprise development came just as jury selection was set to begin.
Last week Mr Roof was deemed competent to stand trial in the shooting of nine Charleston parishioners in June 2015.
Wearing a grey jail-issue jumpsuit, he was sitting on Monday morning at his defence table after his lawyers moved to the side.
Judge Gergel told the court: "I do find defendant has the personal capacity to self-representation."