The men are accused of planning a bizarre and gruesome plot to kill the 18-year-old pop star.
The suspects include a former inmate, his nephew and a man currently serving a life prison sentence.
Authorities say the plot was to castrate Bieber and his bodyguard and then strangle them.
It was supposed to happen last month when Bieber was in Manhattan for two shows at Madison Square Garden.
Prosecutors say the mastermind of the alleged plot is Dana Martin, a 45-year-old man said to be obsessed with Bieber. ABC News reports Martin has a large Bieber tattoo on one of his legs.
Martin is also serving 978 years in prison for raping and murdering a teenager 12 years ago.
Court documents say former inmate Mark Staake and his nephew, Tanner Ruane, were supposed to carry out the gruesome crimes as part of a string of four murders.
Staake was arrested in Vermont on an outstanding warrant. Ruane is in custody near Albany.
All three men face conspiracy and other charges.
Bieber's representatives aren't commenting on the alleged plot, but they did release a statement saying, "We take every precaution to protect and ensure the safety of Justin and his fans."
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