Jake Thomas Patterson allegedly killed Jayme Closs' parents before taping her hands and ankles and throwing her in a car boot.
Jake Thomas Patterson blasted open the family's front door with a shotgun before shooting the couple dead and then kidnapping the 13-year-old last October, investigators said.
According to authorities, Jayme and her mother hid in the bathroom of their home near Barron, Wisconsin as Patterson came to the front door.
Patterson then broke down the bathroom door, shot her mother and taped Jayme's hands and ankles.
He then dragged the girl to his car and threw her in the boot, it is alleged.
Patterson is charged with two counts of intentional homicide, kidnapping and burglary and has appeared in court via videolink.
He spoke only to confirm his name and address were correct on charging documents.
Jayme was missing for almost three months before a woman walking her dog near Gordon, Wisconsin, found her on the road last week.
According to a criminal complaint, Jayme told detectives Patterson would make her hide under his bed in his bedroom when his friends and relatives came over and weights were used to block her.
"When he made her hide under his bed, (Jayme) stated he stacked totes and laundry bins around the bed with weights (like weights for barbells) stacked against them so she could not move them without his being able to detect it if she did," the complaint stated.
On 10 January, Patterson told Jayme he would be gone for five or six hours, and made her go under the bed.
After Patterson left, she pushed bins and weights away from around the bed and crawled out.
She went towards a woman who she saw walking a dog and the woman raised the alarm, the complaint said.
According to the complaint, Patterson told investigators he first spotted Jayme while driving to his job at a cheese factory near Almena, Wisconsin, when he stopped behind a school bus and watched her get on.
Patterson was quoted as saying that when he saw Jayme "he knew that was the girl he was going to take".
He twice went to the Closs home intending to take Jayme but was unable to do so because too many people were around before he was able to kidnap her, the complaint stated.