Interpreting depositional settings of cave sites is generally problematic, especially in absence of paleontological/archaeological evidence. This is the case of some deposits at San Teodoro Cave (Sicily), a key site for the Mediterranean Paleolithic. In a stratigraphic level interrupted by a carbonatic concretion, phosphatic nodules are present only in the part enclosed between the concretion and the cave wall. The discovery of these nodules combined with the punctual lack of fossils had initially suggested an erosion phenomenon and subsequent formation of nodules at a vadose level. Here we show the usefulness of an integrated, geochemical-paleoecological approach in defining stratigraphy and paleoenvironmental reconstructions. XRD, ICP-OES, ATR-FTIR and EDS analyses allowed the formulation of a new hypothesis regarding the origin of the nodules, the depositional dynamics, and the role played by the guano produced by an extensive colony of bats. The role of barium and rubidium in detecting taphonomical processes has been highlighted.