Conley said Hernandez used a handgun to shoot and kill Daniel Abreu and Safiro Furtado, two Cape Verdean nationals, on July 16, 2012, in Boston's South End.
The former tight end for the New England Patriots is already in jail awaiting trial on charges he and two accomplices shot a man to death last June in an industrial park near his home in South Attleboro, Massachusetts. He has pleaded not guilty.
Hernandez's attorney was not immediately available to comment on the new charges.
Hernandez was seen as a rising star in the NFL and had contract with the Patriots worth about $40 million. The Patriots released him from the team hours after his arrest last June.
The murder charges against Hernandez were seen as a setback for the NFL. Despite efforts to protect itself from controversy, the league has been dragged into a string of scandals by players stretching from O.J. Simpson's murder trial in 1995 to more recent cases involving dog fighting, injury bounties, spying and gambling.