Prosecutors charged Brent Zubek with the murders of John David Lee, 40, and Oletta Williams, 28.
He was also charged with assault with a firearm on a peace officer and other charges following a manhunt that ended in a shootout in Encino.
Zubek was shot in the hip by officers after he pulled a gun and pointed it at them. No officers were injured.
Police believe the victims were killed five to six weeks before the decomposed bodies were found on the 20400 block of Lassen Street.
Prosecutors will decide later whether to seek the death penalty. Zubek is being held without bail.