The 9 March attack saw two assailants force their way into a building of the Association of the Grand Temple of Free and Accepted Masons of Turkey, armed with guns and homemade pipe bombs.
One of the bombers and a waiter were killed when the former set off explosives wrapped around his body. The second assailant survived with severe injuries. Five freemasons were also injured.
Turkish authorities blamed the attack on a local cell of the al-Qaida network.
The bomber who survived the blast, Engin Vural, was present in court on Friday.
The indictment referred to ties between Usama bin Laden's network and the local cell held responsible for the attack.
Freemasons are widely considered as pro-Zionist among Islamist circles in Turkey.