Umar Patek, 41, was extradited to Indonesia after his arrest in January in Abbottabad, Pakistan.
While on the run Patek was one of Asia's most-wanted terror suspects and had a $1 million bounty on his head under the US rewards for justice programme.
"Patek's trial has been confirmed for February 13 at the West Jakarta district court," court spokesman Mirdin Alamsyah told AFP Thursday.
Patek could face death by firing squad if convicted of various terror-related charges including bomb-making, premeditated murder, firearms possession and using a false identification.
Prosecutors recommended the court charge Patek with premeditated murder and assembling bombs in attacks on nightclubs on the resort island of Bali in 2002 that killed 202 people, and on churches in Jakarta on Christmas Eve in 2000.
They also allege that Patek tested out three M16 assault rifles to help prepare a terrorist training camp in Aceh province on Sumatra Island, where police say militants were planning gun attacks on prominent Indonesian figures.
Born in 1970, Patek is a suspected member of the al Qaeda-linked Southeast Asian network Jemaah Islamiyah (JI).
Indonesia has waged a successful crackdown on large terror networks and has significantly weakened the JI network, killing top figures in bloody police raids.
Three others behind the 2002 Bali attacks - Amrozi, Mukhlas and Imam Samudra were executed by firing squad in November 2008.
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