The three - John Jodkam, Marshall Magincalda and Jerry Shumate - were among seven marines and one navy corpsman charged with kidnapping and murdering 52 year-old Hashim Ibrahim Awad on April 26.
According to prosecutors, the marines and sailor kidnapped Awad, bound his feet, dragged him from his home and shot him in a roadside hole.
All seven marines have been held at their Camp Pendleton base south of Los Angeles since May.
The ruling came after preliminary hearings were held for Jodkam, Magincalda and Shumate.
Lieutenant-General James Mattis, the commanding general in the case, said he would not seek the death penalty.
The three marines will face other charges that include conspiracy, housebreaking and wrongfully seizing and holding a victim against his will.
The four other marines and the sailor face preliminary hearings in coming weeks to decide if they too should be court-martialed.