The basement underneath Huaynaputina is formed by almost sediments and volcanic intrusions of Paleozoic to Mesozoic age including the Yura Group as well as the Cretaceous Matalaque Formation of volcanic origin. During the Tertiary, these were overlaid by a total of deposits from the ignimbritic Capillune, Llallahui and Sencca Formations. Cretaceous sediments and Paleogene–Neogene volcanic rocks form the high plateau around Huaynaputina. The emplacement of the Capillune Formation continued into the earliest Pliocene; subsequently the Plio-Pleistocene Barroso Group was deposited, which includes the composite volcano that hosts Huaynaputina but also ignimbrites that appear to come from calderas. One such caldera is located just south of Huaynaputina. The late Pleistocene to Holocene volcanoes have been classified as the Arequipa Volcanics.