The Cyclades are part of a metamorphic complex that is known as the Cycladic Massif. The complex formed during the Miocene and was folded and metamorphosed during the Alpine orogeny around 60 million years ago. Thera is built upon a small, non-volcanic basement that represents the former non-volcanic island, which was approximately 9 by 6 km (5.6 by 3.7 mi). The basement rock is primarily composed of metamorphosed limestone and schist, which date from the Alpine Orogeny. These non-volcanic rocks are exposed at the Profitis Ilias Mountains, Mesa Vouno, the Gavrillos ridge, Pyrgos, Monolithos, and the inner side of the caldera wall between Cape Plaka and Athinios.
The metamorphic grade is a blueschist facies, which results from tectonic deformation by the subduction of the African Plate beneath the Eurasian Plate. Subduction occurred between the Oligocene and the Miocene, and the metamorphic grade represents the southernmost extent of the Cycladic blueschist belt.
Volcanism on Santorini is due to the Hellenic Trench subduction zone southwest of Crete. The oceanic crust of the northern margin of the African Plate is being subducted under Greece and the Aegean Sea, which is thinned continental crust. The subduction compels the formation of the Hellenic arc, which includes Santorini and other volcanic centres, such as Methana, Milos, and Kos.
The island is the result of repeated sequences of shield volcano construction followed by caldera collapse. The inner coast around the caldera is a sheer precipice of more than 300 metres (980 ft) drop at its highest, and exhibits the various layers of solidified lava on top of each other, and the main towns perched on the crest. The ground then slopes outwards and downwards towards the outer perimeter, and the outer beaches are smooth and shallow. Beach sand colour depends on which geological layer is exposed; there are beaches with sand or pebbles made of solidified lava of various colours: such as the Red Beach, the Black Beach and the White Beach. The water at the darker coloured beaches is significantly warmer because the lava acts as a heat absorber.
The area of Santorini incorporates a group of islands created by volcanoes, spanning across Thera, Thirasia, Aspronisi, Palea, and Nea Kameni.
Santorini has erupted many times, with varying degrees of explosivity. There have been at least twelve large explosive eruptions, of which at least four were caldera-forming. The most famous eruption is the Minoan eruption, detailed below. Eruptive products range from basalt all the way to rhyolite, and the rhyolitic products are associated with the most explosive eruptions.
The earliest eruptions, many of which were submarine, were on the Akrotiri Peninsula, and active between 650,000 and 550,000 years ago. These are geochemically distinct from the later volcanism, as they contain amphiboles.
Over the past 360,000 years there have been two major cycles, each culminating with two caldera-forming eruptions. The cycles end when the magma evolves to a rhyolitic composition, causing the most explosive eruptions. In between the caldera-forming eruptions are a series of sub-cycles. Lava flows and small explosive eruptions build up cones, which are thought to impede the flow of magma to the surface. This allows the formation of large magma chambers, in which the magma can evolve to more silicic compositions. Once this happens, a large explosive eruption destroys the cone. The Kameni islands in the centre of the lagoon are the most recent example of a cone built by this volcano, with much of them hidden beneath the water.