Jotabeche is a high volcano with a caldera. A rhyolitic dome formed inside of the caldera. The Jotabeche complex reaches a thickness of when including ignimbrite, lava domes and lavas. The high and wide Jotabeche Norte stratovolcano is found northeast of Jotabeche and is surrounded by pyroclastic flows. The Santa Cecilia lava domes () have diameters of and sit along a long fault. 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. N-S to NE-SW trending faults border the volcanic complex and have allowed the intrusion of diorite porphyries. The resulting hydrothermally altered rocks are the sites of mineral deposits and prospects. These faults include the Yeguas Heladas, Rio La Gallina and Rio Astaburuaga and form a hexagonal structure which partly forms the margin of the caldera. Otherwise, only little erosion has taken place at Jotabeche; stronger erosion though has exposed a > thick hydrothermally altered complex at Aldebaran-Cerro Casale. Other hydrothermally altered areas are found within depressions. The crust beneath Jotabeche reaches a thickness of .