The 30-year-old asylum seeker from Chechnya, Magomed Z., was arrested in August in Heidenreichstein, near Gmünd in Lower Austria. He has been held in pre-trial custody in Krems since his arrest.
According to the prosecution, the man fought for Isis in Syria from July to December of 2013.
In addition to being an alleged jihadist, the man is also accused of providing financial support to Syrian fighters, to the amount of €691 (US$800).
A further allegation of procurement and possession of child pornography completes the charge sheet. Public defender Wolfgang Blaschitz says that his client will be pleading not guilty on all charges.
According to a report from the Reuters news agency, the defendant said he had gone to Syria only to help refugees and search for the son of a relative.
"Jihad brings only war, brings only suffering," he said quietly through an interpreter.
"I myself experienced war in Chechnya. I know what happened to us, having nothing to eat. We ate grass. I saw the images of war on the internet and wanted to help."
Magomed, who faces up to 10 years in prison, said he had only done charity work in Syrian refugee camps and did not fight with Isis.
The trial is expected to last one day, with a verdict due by Friday.