La Pacana is situated in a basement formed by various Paleozoic formations and Tertiary ignimbrites and volcanoes.

[7] A number of stratovolcanoes and ignimbrite-forming centres have erupted in the Central Volcanic Zone since the Miocene,[8] about 50 of which are considered to be active.

[16] This resurgent dome is cut by numerous faults and features a poorly developed graben on its summit.

[16] The collapse of the caldera cut through older volcanic centres, exposing the Ceja Alta and Quilapana porphyry deposits.

[21] Some extant hot springs within the caldera may indicate that there is still a geothermal system associated with La Pacana, although not a very important one considering their low temperature (less than 25 °C (77 °F)).

[13] The Central Andes are the site of extensive ignimbrites that were erupted from large calderas usually located within the adjacent Altiplano, east of the principal volcanic arc.

[25] Stratovolcanoes developed on top of these ignimbrite sheets and today form the most clear expression of volcanic activity in the region,[9] with some of them exceeding the height of 6,000 metres (20,000 ft) above sea level.

[25] The long-lasting dry climate means that traces of volcanic activity can be recognizable over long timeframes.

[26] The Altiplano-Puna volcanic complex is underpinned by a large seismic velocity anomaly at a depth of 20 kilometres (12 mi), which may be the largest structure consisting of near-molten (10–20%) rock on Earth.

[15] This partial melt zone was formed by the injection of mafic magmas into the lower crust; a major episode of overturning before 10.6 million years ago caused crustal anatexis and started the onset of ignimbritic volcanism.

[29] Presently, the inferred margin of this partially molten zone coincides fairly well with a negative gravimetric anomaly that clusters around the tripoint between Argentina, Bolivia and Chile and with the extent of the Altiplano-Puna volcanic complex.

[8] Most of this original basement however is covered by Miocene ignimbrites from centres that may coincide with the La Pacana caldera.

[28] Additional volcanic centres west and southwest of La Pacana are Acamarachi, Láscar, Colachi and Cordón de Puntas Negras.

[15] Both the Atana and the Toconao ignimbrite include minerals like allanite, apatite, biotite, epidote, hornblende, ilmenite, magnetite, monazite, orthopyroxene, plagioclase, quartz, sanidine, titanite and zircon.

[15] Ultimately, the magmas at La Pacana are the products of mantle melts interacting with various crustal domains deep in the crust, within the partially molten zone that has been found at depths of c. 20 kilometres (12 mi) beneath the Altiplano-Puna volcanic complex.

[35] This ignimbrite has a volume of approximately 180 cubic kilometres (43 cu mi) and is formed by a lower un-indurated and an upper indurated subunit.

Tube pumices are contained in the lower subunit and in a less than 10 centimetres (3.9 in) Plinian deposit that was emplaced beneath the Toconao ignimbrite.

[15] This flow sheet originally probably covered a surface area of about 7,700 square kilometres (3,000 sq mi), part of which was later eroded away.

[37] After its eruption, wind and water driven erosion occurred on the Atana ignimbrite, carving valleys and yardangs into it.

Such differences concern the degree of welding of the ignimbrite, the occurrence or absence of devitrification and the jointing patterns.

Then a tectonic event, most likely a movement along a fault cutting through the caldera, prompted the rise and eruption of the Atana ignimbrite.

[15] Two potential vents have been found at the northern and western margins of the caldera, where breccia deposits occur within the Atana ignimbrite.

[18] 2.4 ± 0.4 million years ago, the Pampa Chamaca ignimbrite filled the moat between the resurgent dome and the caldera rim.

[18] The 3.49 million years old Tara Ignimbrite from the Cerro Guacha caldera reached the northern margin of La Pacana.