Frank O’Donnell (22) is accused of being among a group of men who went into the building while it was under construction and made threats.
A judge ruled that his case can be dealt with at district court level and adjourned it for Mr O’Donnell to decide on a plea.
The accused is charged with threatening to cause criminal damage at the South Dublin Maktab site in Lucan on January 20 this year.
Mr O’Donnell, of Tor An Rí Lane, Balgaddy Lucan, is also accused of trespassing in a manner likely to cause fear in the same incident.
He first appeared before Blanchardstown District Court earlier this year and the case came back before Judge Gerard Jones for the directions of the DPP to be given.
Garda Sergeant Maria Callaghan said the directions were for the case to be dealt with at district court level subject to jurisdiction being accepted by the judge.
Outlining the allegations, she said gardai took a report that two men were carrying out repairs to the roof of a building that was being converted to be used as a mosque.
Four men including the accused allegedly entered the building and threatened the pair, the court heard.
The accused allegedly said: “you are trying to build a mosque here - you build it and I’m going to f**king burn it.”
According to the prosecution, he again shouted: “you build a mosque here and I’m going to burn it.”
“We will deal with it here,” Judge Jones said, accepting jurisdiction in the case. He ordered the prosecution to disclose evidence to defence solicitor Simon Fleming and adjourned the case to a date in November.
Bail was previously granted with conditions that Mr O’Donnell does not enter the site at South Dublin Maktab and does not loiter in the environs of the site. He must also not interfere with any witnesses involved in the prosecution.
The accused also provided a contact phone number to gardai as part of his bail terms.
Free legal aid was granted earlier after the court heard the accused was not working and was on social welfare. The charges are under the Criminal Damage and Public Order Acts.