A security cordon was thrown around Serang courtroom in west Java, as about 2,000 people held a mass prayer and chanted Koranic verses in solidarity with the accused.
The victims were part of Ahmadiyah sect, who consider themselves Muslims but are considered heretics and blasphemers by conservatives in the Islamic-majority country.
A cleric, Ujang Mohammed Arif, 52, is charged with planning the attack and moblising more than 1,000 people.
Rights groups say violence against minorities in Indonesia have been rising for the last seven years. They hope that the trial will be a first step towards official recognition of violence against religious minorities such as Ahmadiyah and Christians.