The suspects, Benjamin Haskell, 23, Michael Jacques, 24, and Thomas Gleason, 21, were expected to be arraigned in federal court in Springfield later Friday.
The men were charged with violating a civil rights conspiracy statute that makes it illegal to injure, threaten, or intimidate anyone from exercising their civil rights.
It wasn't immediately clear if the men were being charged with setting the fire.
The blaze caused an estimated $2 million in damage. Within hours, state fire investigators called it arson.
The church's pastor, the Rev. Bryant Robinson Jr., said after the fire that he thought it was related to the election of Obama, who will be the nation's first black president.
Robinson said Friday the arrests gave the church a sense of confidence the system doesn't allow people to get away with wrongdoing.
"It was my hope from the very beginning that they might apprehend the culprit or culprits," he said.
