Among the charges are premeditated murder, bomb-making and illegal firearms possession. Patek could face the death penalty.
He is believed to be a key member of Jemaah Islamiah (JI), the militant Islamist group blamed for the attacks and linked to al-Qaeda.
He was arrested in January 2011 in Abbottabad in Pakistan.
In August he was extradited to Indonesia in a move seen at the time as a significant coup for anti-terror agencies in the country.
The BBC’s Karishma Vaswani in Jakarta says the trial is expected to go on for months, with a verdict likely to be delivered at the end of May or early June.
Security analysts believe it was no coincidence that he was caught in the same town in which al-Qaeda leader Osama Bin Laden was later killed.
Officials cannot confirm whether the two met, before Bin Laden was killed in a raid by United States forces in May 2011.