The highest mountain of the Sahara, the volcano is one of several in the Tibesti range, and reaches an elevation of 3,447 metres (11,309 ft), rising 3 km (1.9 mi) above the surrounding sandstone plains.

Within it on the southeast side is a smaller caldera known as Era Kohor, about 2 kilometres (1.2 mi) wide and 350 metres (1,150 ft) deep.

Era Kohor contains trona deposits, and Emi Koussi has been studied as an analogue of the Martian volcano Elysium Mons.

[7] Volcanism in this area is poorly studied; as the region is remote and access difficult for political reasons.

[12] Emi Koussi rises to a height of 3,415 metres (11,204 ft) on the southern side of the volcano,[13][14] towering 3 kilometres (1.9 mi) above the surrounding terrain.

[13] Trachytic lava flows are exposed in its walls,[19] and sodium carbonate has been deposited on its floor,[24] which lies at an elevation of 2,670 metres (8,760 ft)[20] and contains a salt lake.

[25] The Kohor pumices and two sets of ignimbrites cover the flanks of Emi Koussi,[18] which steepen as they approach the summit.

[30] The oldest rocks below the Tibesti are Precambrian diorites, granites and schists,[27] which are probably of Neoproterozoic age and are differentiated into two units.

Phenocryst chemistry and content varies between the various rocks; among the minerals are alkali feldspar, amphibole, biotite, clinopyroxene, olivine, oxides and plagioclase.

Alkali feldspar, apatite, clinopyroxene, olivine, magnetite, mica, nepheline, oxides, plagioclase, quartz, sodalite, titanite and zircon also form the groundmass of microliths in erupted rocks.

[17] Elleboe wadi originates on Emi Koussi,[38] and several streams on the western flank join into the Enneri Miski which drains southwards and disappears south of the mountains.

[44] Radiometric dating has yielded ages of 2.42 ± 0.03 - 2.33 ± 0.09 million years ago for the oldest Emi Koussi stage.

The third stage has yielded ages of 1.4 ± 0.3 - 1.32 ± 0.2 million years ago;[15][45] formerly Era Kohor was considered to be a Holocene centre.

[24] During the first stage, Emi Koussi erupted trachytes and trachyandesites in the form of ignimbrites and basaltic lapilli.

[47] Early in the Pleistocene, erosion took place on the flanks of Emi Koussi,[5] and carbonates were deposited in Era Kohor until recent times.

There are no weather stations close to Emi Koussi and the stations at lower elevations likely underestimate precipitation at higher elevations,[39] but based on cloud cover data, a yearly precipitation of 80–120 millimetres (3.1–4.7 in) has been estimated for Emi Koussi;[53] in the past it was wetter than this.

[56] The diatom fauna appears to be unusual in comparison to other Saharan paleolakes, probably owing to the high elevation of the Emi Koussi lake.

[60] The summit region features montane vegetation,[61] including Artemisia-Ephedra steppes[62] which cover large parts of the caldera floor[47] and may have been used as pastures.