The court documents don't say whether Doyel confessed to the killing. Prosecutor Alicia Cook would say only that some murder cases can be proven with circumstantial evidence.
Defense attorney Todd Utzinger didn't immediately return a message seeking comment.
Doyel, 47, was being held in the Salt Lake County jail. The murder charge carries a punishment of 15 years to life in prison, if convicted. State obstruction of justice and theft charges also were filed against him.
Doyel earlier pleaded not guilty to a federal kidnapping charge involving Jones, which carries a maximum punishment of 20 years in prison but can lead to the death penalty in some circumstances. An autopsy found Jones probably died three days before her body was found.
Doyel is also charged in state court with kidnapping a woman who was a passenger on the cross-country trip. She told authorities she didn't know about the body.
At a court appearance April 30 on the federal charge, Doyel blurted out a series of odd statements, including that Jones was still alive, and said the federal complaint against him was a lie. Utzinger claimed Doyel has a history of mental illness.
In court documents, investigators said Doyel stole money from Jones and moved out of the home they shared after several arguments. Jones disappeared after meeting with police April 16 to ask about a protective order.
Authorities said Doyel used Jones' cell phone after she disappeared to send text messages to her friends and family declaring she was fine. He covered the clothing with a deodorant stick to mask the smell and used air freshener and perfume on the box, according to an FBI affidavit.