The AKP's rise to power concerned the military, which has unseated four governments since 1960, under the auspices of protecting Turkey's secular constitution.
Ilnur Cevik, a chief columnist with the newspaper New Anatolian, told Al Jazeera: "I think that this is a kind of reconciliation between the military and the civilian government.
"There is a kind of war going on between the Turkish military and the Erdogan government for, I think, domination of power."
"Turkey has been phasing out its military’s influence on politics and Erdogan [Turkey's prime minister] has been successful … throughout the year there has been a lot of court cases against military personnel," Cevik said
The plot allegedly involved plans to bomb historic mosques and provoke Greece into shooting down a Turkish war plane to create a war-like situation and destabilise the AKP, media reports said.
Cetin Dogan, a four-star general, the first army commander and the alleged mastermind of the plan, was arrested last month and hospitalised the following day with heart problems.
He has denied the charges, arguing that papers from a contingency plan based on a scenario of domestic unrest were doctored to look like a coup plot.
Some analysts said the charges may have been an attempt by the AKP government to block the advancements of military officers it considered unfriendly.
Officers on the arrest warrant were recently passed up for promotion.
A total of 196 suspects were initially charged in the case, in some of the toughest judicial actions ever taken against Turkey's influential military.
Trials for the remaining suspects are due to begin on December 16.
Public opinion has been split on the case, with AKP supporters and some liberals viewing it as a step forward for democratic accountability and civilian control over the military, while others view the arrests as an attempt to silence critics of the government.
More than 400 people, including pro-secular academics, journalists and politicians and soldiers, are already on trial over separate charges of plotting to bring down the government.