The six women and 10 men are charged with hate crimes motivated by religious differences, conspiracy and assault.
The suspects are also accused of trying to destroy evidence, including a camera, shears and a bag of hair.
Prosecutors say the attacks were part of a feud directed by a breakaway Amish bishop, Sam Mullet.
The updated indictment in Thursday's court hearing also alleges that Mr Mullet lied to federal officials.
The judge set the trial for 27 August. The accused face up to 10 years in prison if found guilty.
Mr Mullet told the Associated Press in October that he did not order the attacks, but did not stop his sons and others in his group from carrying them out.
The Amish leader said in the interview that he had wanted to send a message that the others should be ashamed for the way they had treated his group.
Jefferson County Sheriff Fred Abdalla told journalists that Amish communities in the area had been left terrified by the attacks.