Ahmed Abu Khattala, 43, appeared in court on 17 new charges, some of which may be punishable by death.
He did not speak during the hearing in Washington but his lawyer entered the plea on his behalf.
US Ambassador Chris Stevens and three others were killed in the attack, which became a political lightning rod.
The new charges include four counts of killing a person in the course of an attack on a federal facility.
Other new charges levelled against Mr Khattala include one count of murder of an internationally protected person and one count of providing material support and resources to terrorists resulting in death.
Previous charges denied by Mr Khattala include providing material support and resources to terrorists including himself; killing a person on a federal facility; and damaging property of the US by fire and explosives resulting in death.
???Native of Benghazi in eastern Libya
???Construction worker by trade
???Spent several years in Col Muammar Gaddafi's notorious Abu Salim prison in Tripoli
???Formed his own small militia during the anti-Gaddafi uprising
???Denies any links to al-Qaeda but has expressed admiration for it
???Also denies any role in the attack on the US embassy in 2012, but eyewitnesses report him being there
???US state department says he is a senior leader in Islamist group Ansar al-Sharia
Profile of Abu Khattala
Mr Khattala was taken into custody in a secret US military raid in Libya on 15 June. He was subsequently indicted on 26 June in connection with the attack on the US facility.
On 11 September 2012, gunmen stormed the US consulate in Benghazi and set it on fire.
In addition to Mr Stevens, information technology specialist Sean Smith and security workers and ex-Navy Seals Tyrone Woods and Glen Doherty were killed.
The White House initially said the attack stemmed from anti-American protests over a crude video produced in the US that was deemed insulting to Islam.
Government investigators soon determined it was an organised attack planned by local militias.
In subsequent years, Republicans have accused President Barack Obama's administration of compromising security, a failure of intelligence and covering up the involvement of militant groups in order to assist the president's re-election campaign.
The suspected ringleader of the September 2012 raid on a US diplomatic post in the Libyan city of Benghazi has pleaded not guilty to all charges.