Prosecutors accuse the military leaders of plotting to blow up mosques and provoke tensions with Greece in order to foment unrest and topple the government.
They are seeking 15-to-20-year jail sentences for those involved in the plot.
A total of 196 defendants will stand trial in connection with the plot. The first hearing in the case is scheduled for December 16.
The investigation is the Turkish government's strongest action to date against the country's powerful military, which has staged four coups over the last 50 years.
Many of Turkey's senior military officers are staunch secularists who worry that AKP, which has Islamist roots, will break down the traditional barrier between religion and state.
Dozens of professors, journalists and other public figures have been arrested in connection with a separate organisation, called "Ergenekon," which has been vaguely accused of plotting against the government.