Yates was arrested on April 18, 2000, for the murder of Jennifer Joseph. After his arrest, a search warrant was executed on a 1977 white Corvette that he had previously owned. A white Corvette had been identified as the vehicle in which one of the victims had last been seen. Coincidentally, Yates had been pulled over in this vehicle while the Task Force was searching for it, but the field interview report was misread as saying "Camaro" not "Corvette," thus the incident was not realized until after Yates had been arrested.
After searching the Corvette, police discovered blood that they linked to Jennifer Joseph and DNA from Yates that they then tied to 12 other victims. In 2000, he was charged with 13 counts of first-degree murder and one count of attempted first-degree murder in Spokane County Superior Court. As part of a plea bargain in which Yates confessed to the murders to avoid the death penalty, he was sentenced to 408 years in prison. Charges were dropped in the murder of Shawn McClenahan, however in a statement made by Yates, he apologized to her family and the other victims.