The Turkish government is meeting armed forces chiefs to discuss forthcoming senior military appointments.
The BBC reports civilians are in charge of the process for the first time.
Prime Minister Recep Tayyip Erdogan has convened a four-day annual meeting to decide on military promotions.
The chiefs of the armed forces and the army, navy and air force resigned on Friday.
The military and the AK party have for the past two years been engaged in a war of words over accusations that parts of the military had been plotting a coup.
Some 250 officers are in prison on charges linked to various anti-government plots dating back to 2003.
A BBC correspondent says the dispute has now come to a head and Mr Erdogan has won.
Military intervention in politics has been a hallmark of modern Turkish history.
President Gul last week appointed General Necdet Ozel, 61, as the new army chief.
General Ozel is widely expected to be swiftly elevated to become the new chief of the general staff. Tradition dictates that only the head of the army can take over the top job.
He was previously commander of Turkey's Aegean Army from 2007-2008 and head of the 2nd Army from 2008-2010, before becoming Gendarmerie commander in August 2010.