The grievances are for Hernandez's 2013 base salary ($1.323 million) and his 2014 salary ($1.137 million) and workout bonus ($500,000), which had guarantee language attached to them in his original contract, and for the final installment of his signing bonus ($3.25 million).
Hernandez has pleaded not guilty to first-degree murder in the death of Odin Lloyd, a 27-year-old semi-pro football player from Boston.
In August, the NFLPA had filed a grievance against the Patriots on behalf of Hernandez, seeking to collect $82,000 in workout bonuses.
"On behalf of all players, it is our responsibility to protect the rights in the collective bargaining agreement," the union said in a statement at the time of the first grievance. "We are not tone-deaf to what the allegations are in this case, but for the benefit of all players, there are important precedents here we must protect."
A team can recover bonus money and avoid a cap hit if a player violates one of the league's personal-conduct policies or defaults on contract language.
Patriots owner Robert Kraft later responded to the grievance, saying: "Simple: you can look at our history. We honor all of our contracts, and we expect the people who sign them to honor their part of their contract."
Hernandez signed a five-year extension in August 2012 that was to keep him with the Pats through 2018. The extension had a total maximum value of $40 million, with a $12.5 million signing bonus.