Stein, 33, was in a relationship with Kallista Mutten, who he maintained throughout a four-week murder trial was the person who murdered the girl.
Police located Charlise's body on January 18, 2022, near the Colo River, northwest of Sydney, with close-range gunshot wounds to her face and lower back.
Charlise Mutten had been visiting her mother Kallista over Christmas when she went missing. (HANDOUT/NSW POLICE)
The jury rejected Stein's version of events, in which he admitted to dumping the body, but claimed Ms Mutten shot her daughter and placed her corpse in a barrel on the back of his ute without his knowledge.
After deliberating for almost two weeks, the jury on Wednesday morning delivered a unanimous guilty verdict after which Stein was formally convicted in the NSW Supreme Court of Charlise's murder.
During the trial, Ms Mutten broke down crying in court as she was forced to deny killing her daughter.
"Are you serious?" a devastated Ms Mutten asked Stein's lawyer.
"I didn't even know where she was shot, so now I know."
Justin Stein tried to blame Charlise Mutten's mother Kallista for the murder. (Bianca De Marchi/AAP PHOTOS)
Stein also appeared to shed tears as he gave a fabricated version of Charlise's death to the court during his two days in the witness box, saying he was working in a shed when he heard a gunshot.
"That's when I heard Charlise screaming, 'mummy, no', and then bang, there was a second gunshot," he said.
Police received a call on January 14, 2022, from Ms Mutten reporting her daughter missing, sparking an intense four-day search of bushland surrounding the Blue Mountains property where the group had been staying.
Charlise had been visiting her mother and Stein over Christmas from the Gold Coast, where she lived with her grandparents.
She spent the night of January 11 alone with Stein at Mount Wilson, while her mother stayed at a caravan at the Riviera Ski Park, about a 90-minute drive away.
Justin Stein was captured on CCTV towing a boat, with Charlise Mutten's body in a covered-up barrel. (HANDOUT/NSW POLICE)
Toxicology results revealed Charlise had traces in her body of the anti-psychotic drug Seroquel, for which Stein had a prescription to treat schizophrenia.
Crown prosecutor Ken McKay SC told the 12-person jury it was possible Stein killed Charlise when she became sick after he gave her the drug, although he noted the prosecution did not have to prove a motive.
An adult dose of the drug would have a profound sedating effect on a child, the court heard.
The same day Charlise's body was found, investigators arrested and charged Stein with her murder after using location data from his phone to pinpoint where the barrel was dumped.
Justin Stein was arrested on the day Charlise Mutten's body was found. (HANDOUT/NSW POLICE)
Stein would later admit to dumping the body, but he claimed he panicked after discovering it on the back of his ute.
Ms Mutten said the morning after Stein murdered Charlise, he told her the girl was sick and he left her with a woman who was valuing property at the Mount Wilson estate.
He later changed his story, telling the increasingly frantic mother it could have been his former criminal associates who took Charlise, convincing her not to call police for fear they might kill the girl.
Stein initially gave police the same account about leaving Charlise with the property valuer before changing his story and pointing the finger at Ms Mutten.
The Mount Wilson property where Charlise Mutten was alone with Justin Stein. (HANDOUT/NSW POLICE)
He claimed Ms Mutten told him to lie to police about leaving Charlise with the property valuer and that she had come up with a plan for him to pretend to look for the girl.
While Stein was tracked driving to boat ramps across Sydney with Charlise's body in his ute, he was also sending Ms Mutten texts suggesting he was "going to war" to look for the nine-year-old.
Stein will return to court for a sentence hearing on August 23.
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