The Tibesti mountains feature a desert mountain climate. There are no weather stations close to Emi Koussi and the stations at lower elevations likely underestimate precipitation at higher elevations, but based on cloud cover data, a yearly precipitation of has been estimated for Emi Koussi; in the past it was wetter than this. The climate reflects both northerly and southerly influences and is distinct from that of the surrounding deserts. There is no evidence of nivation forms on Emi Koussi and the identification of periglacial landforms is questionable, although periglacial activity likely occurred in the Pleistocene and may continue to the present-day. Even during the Pleistocene, no part of the mountain had sub-freezing temperatures through the entire year.