In this paper, we present old and new data about our integrated interdisciplinary stratigraphic study of sedimentary deposits preserved in the Grotta dei Baffoni Cave of the Frasassi hypogenic cave complex, including sedimentological, paleontological, archaeometric, and radiometric analyses. This research work allowed us to reconstruct the geologic, environmental, and human history of this part of the northeastern Apennines of Italy for the past 200,000 years, from the late Middle Pleistocene to the Present. Accumulation of alluvial sediment began in this cave ~200,000 years ago, when an entrance was breached by the Sentino River during its process of incision and deepening of the Frasassi Gorge coupled with regional tectonic uplift. Flooding of the cave went on until the entrance sill of the cave was lifted up to an elevation that could no longer be reached by the river, sometime in the mid–Late Pleistocene. After this, windblown dust (i.e., loess) and coarser carbonate clasts derived from the disintegration of the vaults due to cryogenic processes and/or seismically induced collapses of the limestone vaults, accumulated on this now-dry underground environment. The stratigraphy of an ~4-m-thick sedimentary deposit accumulated in the vast atrium room of the cave was measured, sampled, and documented in two excavation trenches in 1952 by archaeologist Anton Mario Radmilli. By collecting a dozen stratigraphically located osteological finds for ¹⁴C dating, and revisiting artifacts collected by Radmilli, which are archived respectively in the Museum of Natural History of Verona and in the National Museum of Archaeology of Ancona, we assessed that the cave was frequented by wild animals, such as cave bear and ibex, starting in the mid–Late Pleistocene. Dating of charcoal particles from subsurface sediments in the inner part of the cave suggested that fires were lit in this cave by Epigravettian visitors during the Younger Dryas cold period. Scarce archaeological evidence nevertheless suggests that man began using this underground environment for worship practices probably in the early Neolithic. Human bones in the lower part of one of Radmilli's excavations yielded early Eneolithic ages. No other human bones were found in overlying levels of this excavation, but the typology of animal bones and associated ceramic artifacts, corroborated by our ¹⁴C dates, suggest that this cave was utilized as a worship or ritual place until the early Middle Bronze Age. After that, the cave was sporadically used as a shelter for herders until recent times.