Justin Laurens Stein, 33, has pleaded not guilty to murdering the schoolgirl on or around January 12, 2022, at Mount Wilson, in the Blue Mountains west of Sydney.
His lawyer told the NSW Supreme Court earlier this week that Charlise's mother Kallista Mutten had shot her.
The nine-year-old had been visiting Stein and her mother over the holiday break, with the group spending time between a property at Mount Wilson and a caravan at the Riverview Ski Park, about 90 minutes away.
Ms Mutten and Stein were in a relationship, after meeting while both were serving jail time.
An expected six-week murder trial will continue on Wednesday, with more evidence due from witnesses including Ms Mutten.
Charlise's grandfather, Clinton Mutten, with whom she had lived along with her grandmother since aged four, told the court on Tuesday his daughter had struggled with drug use and had willingly given over care of Charlise.
"Kallista realised that she wasn't providing adequate care," Mr Mutten said.
"She was quite happy for Charlise to come and live with us."
Despite this, he said Charlise and her mother spoke regularly and had maintained an "unconditional" bond.
Charlise had also "really liked" Stein, he told the court.
Charlise travelled from the Gold Coast to Sydney as an unaccompanied minor in December 2021 with plans to spend Christmas and New Year's Eve with her mother and Stein.
The nine-year-old was reported missing on January 14.
On the evening of January 12, Charlise travelled back to Mount Wilson with Stein alone, while Ms Mutten remained at the caravan, prosecutors said.
CCTV images captured the 33-year-old at a service station next day towing a boat with his Holden Colorado ute, which was also allegedly transporting a barrel containing Charlise's body.
The barrel was found near the Colo River, northwest of Sydney, on January 18.
She had been shot once in the head and once in the lower back.
