Following the collapse of the Soviet Union in the early 1990s, independent Azerbaijan and Georgia launched their new national energy policies. This enabled them to bring Western investment and technologies into their energy sectors, which led to the construction of the Baku-Tbilisi-Ceyhan, Baku-Supsa and Baku-Tbilisi-Erzurum pipelines. These pipelines empowered Azerbaijan and Georgia as politically and economically independent actors in regard to the transportation and supply of Caspian’s energy resources to the West. With Turkey’s involvement, the cooperation acquired a larger scope and led to the implementation of the Southern Gas Corridor. However, the regional and national level security threats in the Southern Caucasus including Armenia’s occupation of Azerbaijani territories, the post-2008 Russia-Georgia War situation and its implications, ongoing skirmishes in/around Nagorno-Karabakh, and bomb attacks on pipelines in Turkey brought the security of critical energy infrastructure onto the agenda of regional states, Europe, and even NATO. The national and political security environment in Azerbaijan and Georgia, as well as in Turkey, has therefore become important for European energy security. This requires NATO’s involvement in the protection of energy infrastructures in the South Caucasus region. This article examines, therefore, the possible modes of cooperation between NATO, Azerbaijan and Georgia on the protection of energy infrastructures in the light of the security threats in the South Caucasus. The paper elaborates and concludes with recommendations for deepening the cooperation between NATO, Azerbaijan, and Georgia on energy infrastructure protection.