Deputies suspect that Joseph Dorsey killed 47-year-old Christine Stewart before taking her body to a Poway motel. He was charged in the murder Friday.
Dorsey checked into the motel last weekend, but never checked out. Hotel workers found Stewart's body Wednesday.
Stewart was first reported missing Aug. 4, the same day she and Dorsey were last seen together near a business complex in Canyon Lake.
Dorsey, 27, was last seen driving a dark blue Ford Explorer with grey primer on the hood and California license plate 6UDY773.
The Associated Press contributed to this report.