Prosecutors have charged the 27-year-old identified only as Hassan F. with participating in the beheading of a religious leader in the city of al-Sukhnah in Homs province and involvement in the killings of at least 25 people.
They say at least six women and one child were among the dead in slayings intended as revenge and to terrify the local population.
Prosecutors said it was Hassan F.'s job to compile a list of those to be killed, which was then approved by IS leaders, and oversee the killings.
"I committed nothing," said Hassan F. said at the start of the trial. "I just want my family."
During the court session, gruesome video was shown of the beheading allegedly committed by Hassan F. and another man. Hassan F. denied being in the video or knowing anyone else in the video.
Hassan F. also denied prosecutors' claim that he was a member of a small, armed IS unit.
During his initial testimony, Hassan F. asked not to be executed, but the judge explained to him that there is no death penalty in the European Union.
Hassan F.'s father told the court his son had been imprisoned in Syria for refusing to join IS.
Hassan F. also claimed repeatedly while being questioned by the judge that he was mistreated by police and in jail and that he feared being poisoned. His lawyer said Hassan F. had attempted suicide in prison.
The defense lawyer asked the court to reject many pre-trial statements implicating his client, in part because they were by people who did not personally witness the alleged crimes, or because they had failed to provide any details of the events.
Hassan F., who obtained refugee status in Greece, was initially apprehended in December at Budapest's Ferenc Liszt International Airport when he and a female companion were found to have forged personal IDs.