The crust beneath Jotabeche is 70 kilometres (43 mi) thick, which has had effects on the rock composition of the volcano.
Jotabeche is located at the extreme southern end of the Central Volcanic Zone (CVZ) of the Andes.
The so-called Abancay deflection separates the CVZ in the north from the Peruvian flat subduction segment where no volcanic activity occurs, while the southern limit is marked by a seismic discontinuity around 27° S.[3] Jotabeche is a 5,862 metres (19,232 ft) high volcano with a caldera.
[4] The Miocene volcanic complex branches out in four chains stretching in east-west direction, the Cadillal, Aguas Blancas, Jotabeche Norte and Cordon de Yeguas Heladas.
[2] N-S to NE-SW trending faults border the volcanic complex and have allowed the intrusion of diorite porphyries.
[4] Jotabeche is a volcanic centre in the 26-6 mya old and 200 kilometres (120 mi) long Maricunga belt.
Some stratovolcanoes in the belt include Copiapó-Azufre, Cerros Bravos, Doña Inés, La Laguna, Lagunillas, Ojos del Maricunga, Santa Rosa and Cadillal-Yeguas Heladas.
[7] Jotabeche is located at the southern end of the Maricunga belt, which was active starting from the Oligocene until the Pliocene.
[7] Volcanic activity at Jotabeche is coeval with the last mineralization phase of the Vallecito system in the El Indio belt.
Diorites are also found but the only weak erosion and thick late Miocene rock cover bury them.
[4] The rocks of Jotabeche have lanthanum, strontium and yttrium concentrations which fit an eclogitic trend, similar to other Andean volcanoes Pircas Negras, Tortolas and Vallecito.
[17] More generally, the geochemistry is indicative of the volcanic activity being influenced both by a thick crust and other factors of crustal contamination.
[10] The end of volcanic activity at Jotabeche occurred at the same time as the northeastern arm of the Juan Fernandez ridge passed beneath the volcano.
5.9–6.2 mya the Jotabeche ignimbrite covered a surface area of 3.18 square kilometres (1.23 sq mi).
[4] The so-called Pircas Negras andesitic lava flows occur at the same time as the younger Jotabeche activity.