Che Cruz, 20, pleaded not guilty to the charges Monday afternoon, and his bail was set at $160,000. He was arrested Friday after he returned to Gomez's home just hours after he was released from jail in a case in which he was ordered to stay away from her.
The Los Angeles district attorney's office said Cruz jumped the fence at Gomez's home before his second arrest.
If convicted, he faces up to four years in prison. He is due back in court April 17.
Cruz was first arrested after breaking into Gomez's guest home March 30, and he acknowledged in court Wednesday that he trespassed at her property. He was ordered to stay away from Gomez and her home, was put on probation, and was sent to jail for up to 45 days, but he was released two days later.
Within hours of his release, sheriff's deputies re-arrested Cruz at Gomez's home in Calabasas.
Gomez, the former "Wizards of Waverly Place" actress turned pop star, was at home when Cruz was arrested the first time after he broke into her guest house. It was unknown whether Gomez was home during Friday's intrusion.