Following a two-year visit to Sicily, where he witnessed the March 1638 eruptions of Aetna and Stromboli, Kircher became increasingly fascinated with geological and meteorological phenomena. Upon his return to Naples, he had himself lowered into the active crater of Vesuvius to make firsthand observations. From his investigations and research, Kircher concluded that continually circulating channels of fire (for which volcanoes act as occasionally emerging safety valves) and water honeycombed the Earth's interior, and that these, in conjunction with the wind, were responsible for all weather and geological events.

These ideas formed the thesis of Kircher's most popularly successful and renowned book, Mundus Subturraneus. While primarily a geological textbook, this massive and copiously illustrated volume contained discussions of gravity, the moon, the sun, eclipses, ocean currents, hydraulics, saline analyses, fossils & petrifaction, remains of giants, subterranean beasts and demons, poisons, metallurgy, the Universal Seed, the generation of insects, astrological medicine and fireworks, as well as a lengthy attack on the alchemy of Paracelsus, which Kircher disdains in favor of chymiotechnicus, or 'true chemistry'. While considering the Philosopher's stone 'mystic and fictitious', Kircher himself claimed to have performed palingenisis, resuscitating a plant from its ashes and displaying the results in the Museo Kircheriano until cold weather shattered its glass display vessel.