Among 163 charges, Nicholas Adam Beer (35) is accused of sexually penetrating a child under 13 years and filming the victim more than 150 times.
He is due to reappear in Joondalup Magistrates Court on September 25.
Banksia Grove pastor David Volmer has pleaded guilty to 12 offences, including drugging and raping the girl.
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READ NOWHe is due in Perth Magistrates Court on Friday.