Hakobyan then served in the Soviet armed forces stationed in Afghanistan during the Soviet–Afghan War as deputy commander of a rifle company.

In 1988, he returned to the Transcaucasian Military District to serve as company commander with the 366th Motorized Rifle Regiment, stationed in Stepanakert.

[6] On 18 November 2020, during the political crisis created by the 2020 Nagorno-Karabakh ceasefire agreement, he submitted his resignation from the post of Head of the Military Control Service of the Armenian Ministry of Defense.

[3] Hakobyan gave a press conference following his resignation where he alleged a number of failures by Nikol Pashinyan's government in the 2020 Nagorno-Karabakh war.

[7][8] On 3 May 2021, Hakobyan was charged with revealing state secrets and summoned by Armenia's National Security Service for questioning.