Richard A. Franco pleaded not guilty to the additional charge of burglary on Wednesday.
He is accused of being in the guest house of Berry's Hollywood Hills home earlier this month.
He now faces two felonies stemming from three incidents.
Berry has written in court filings that she is "extremely frightened" of the 27-year-old. She says he nearly gained entry into her kitchen before she was able to lock the door.
Criminal and civil judges have issued restraining orders against Franco in case he is released.
He has pleaded not guilty to stalking the actress and is due in court on Aug. 4.
The Associated Press contributed to this report.