Prosecutors have accused Hernandez of killing Daniel de Abreu and Safiro Furtado in a drive-by shooting on July 16, 2012.
After being read the two charges of first-degree murder in court Wednesday, Hernandez responded "not guilty" to both. He also pleaded not guilty to five other counts.
Hernandez is already in a suburban Boston jail on charges stemming from the June 2013 murder of Odin Lloyd, a 27-year-old semi-pro football player from the Boston area who was dating the sister of Hernandez's girlfriend.
Magistrate Gary D. Wilson ordered Hernandez held without bail for the new charges. The next court date in the Boston case is scheduled for June 24.
Following the pleas of not guilty, assistant district attorney Patrick Haggan detailed the events leading to the shooting, some of which were revealed during DA Daniel F. Conley's news conference after the May 15 indictment.
Haggan said witnesses and surveillance video provided investigators with evidence that Hernandez and an associate met the two victims and three of their friends in a chance encounter at a Boston club in the early morning hours of July 16.
According to Haggan, the evidence suggested that Hernandez felt he was being disrespected by one of the victims at the club. Hernandez believed he was deliberately bumped by one of the victims, forcing him to spill his drink.
There was no verbal argument and Hernandez quickly left the club after only a few minutes. Hernandez, according to Haggan, went to another club and thought he was being followed by the victims.
After de Abreu and Furtado left the club with their friends, Hernandez waited for them to drive away.
Hernandez, prosecutors said, had retrieved a .38 caliber revolver that was stored under the hood of his car and trailed the victims' vehicle in his SUV. He then pulled up alongside the victims' vehicle, pointed the gun out the window and yelled "Yo, what's up now (expletive)," and fired five times.
After Haggan finished, defense attorney Charles Rankin raised an objection, saying the assistant DA's speech with the media in attendance was a "poisoning of the jury pool" and that it presented only a "one-sided view of the case."
Magistrate Wilson countered by saying the prosecution is allowed to detail its case during the arraignment and the "press is always welcome" because it is an open proceeding.
During his May 15 news conference, Conley said the nearly two-year investigation featured testimony from more than two dozen witnesses.
The other charges levied against Hernandez included three counts of armed assault with intent to murder and one count of assault and battery with a dangerous weapon.
Hernandez, who had signed a $40 million contract with the Patriots just months after the Boston double murders, was released by New England just hours after he was arrested for the Lloyd murder.
Authorities have not said whether the two cases are connected.