Gary Gravelle, 51, was indicted on 16 counts, including that he threatened the president in September 2018 by sending an envelope containing white powder and the handwritten message "You Die."
He sent similar envelopes to a synagogue, a mosque and a chapter of the National Association for the Advancement of Colored People (NAACP), according to the indictment.
The note claimed the power was a biotoxin but it was found to be harmless, officials said.
Gravelle also sent emails and made phone calls threatening to detonate bombs in Vermont, Washington and at various locations in Connecticut, including government buildings and a mental health facility.
If convicted of all 16 counts, he could face a maximum prison sentence of 140 years.
Gravelle was previously sentenced in 2013 for sending threatening communications and had been released under federal supervision until his arrest on the new charges last year, according to U.S. Attorney John Durham's statement on Friday.
It was not immediately clear if Gravelle had a lawyer.