The Winterthur public prosecutor's office said in a statement on Friday that the imam was charged on August 2nd with inciting the murder of non-practising Muslims.
He is also accused of having posted violent images of murders on Facebook and giving them to other people.
In addition he faces a charge of violating the Aliens Act by working without a permit.
The public prosecutor is demanding a suspended prison sentence and the man's expulsion from Switzerland with a 15-year ban on returning.
The imam has been under investigation since early November 2016 when police raided the An'Nur mosque after receiving evidence about a sermon given by the imam in which he called for the murder of Muslims who refused to take part in common prayer.
The imam and three others were arrested during the raid.
Proceedings against two of the three were terminated on July 18th, the prosecutor said. The investigation against the third is nearing completion.
In February police arrested ten other people in connection with a brutal attack on two Muslims who are thought to have tipped off a journalist about the controversial sermon.
The An'Nur mosque closed its doors in late June after the landlord of the building refused to extend the rental contract.
The mosque was a controversial presence in the northern Swiss city over allegations that it had connections to terror groups and supported the radicalization of young people.
The mosque denied the accusations.