Many of the 486 suspects face life terms in prison for crimes that include violating the Constitution, murder, attempting to assassinate the president and attempting to overthrow the government.
The trial is one of dozens underway in Turkey in relation to the coup attempt on July 15, 2016, that resulted in 249 deaths. Some 30 coup-plotters were also killed. The government says the coup was carried out by followers of Gulen's movement.
The government says the coup-plotters used Akinci air base as their headquarters. Turkey's military chief Gen. Hulusi Akar and other commanders were held captive for several hours at the base on the night of the coup.
On Tuesday, a group of 41 defendants were paraded from their jail to a courthouse that was built especially at a prison complex to try the coup plotters. They were handcuffed, with two paramilitary police officers on each arm, and protected by armed special force officers.
A total of 461 defendants are behind bars while 18 were freed pending the outcome of the trial. Seven others, including Gulen and an alleged top operative in his movement, are still wanted by the Turkish authorities and are being tried in absentia.
Ozturk, the former air force commander, is also on trial in a separate case, accused of being a ring-leader of the coup.
The families of those killed or wounded during the coup attempt staged a protest Tuesday. Some threw ropes toward the defendants, demanding that the government reinstate the death penalty and that those convicted be hanged. Others threw stones or tried to break through police lines to reach the suspects, shouting "Murderers!"
A total of 1,300 security personnel were deployed both inside and outside the courtroom, the state-run Anadolu Agency reported.
The government declared a state of emergency following the coup and embarked on a large-scale crackdown on Gulen's network and other opponents, arresting more than 50,000 people and purging over 110,000 others from government jobs.
Associated Press writer Suzan Fraser in Ankara, Turkey contributed.