The 5-year-old disappeared from her Fayetteville home on November 10, and her body was found days later in a wooded area just south of Sanford.
According to court documents, 29-year-old Mario McNeill killed the girl the same day she was reported missing.
Shaniya's mother, 25-year-old Antoinette Davis, is charged with human trafficking and child abuse involving prostitution.
Search warrants in the case released Thursday say detectives found nude images of a young girl on McNeill's cell phone. The warrants didn't say if investigators believe the images are of Shaniya.
McNeil is being held in a state prison in Raleigh until his trial.