Vincent Lang, 60, is facing civil rights charges in connection with the July 5 incident.
The indictment says Lang maliciously attempted to damage and destroy the center along the 1400 block of Tyson Avenue by fire, and that he did it because it was a mosque.
Police say surveillance images show him lighting a fire and throwing it into the entryway.
If convicted, Lang faces a maximum of 40 years in prison, with a five-year mandatory minimum.
He's been in federal custody since July 16.