© 2017 Alcaraz-Castaño et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Introduction and objectives Although the Iberian Peninsula is a key area for understanding the Middle to Upper Paleolithic transition and the demise of the Neandertals, valuable evidence for these debates remains scarce and problematic in its interior regions. Sparse data supporting a late Neandertal persistence in the Iberian interior have been recently refuted and hence new evidence is needed to build new models on the timing and causes of Neandertal disappearance in inland Iberia and the whole peninsula. In this study we provide new evidence from Los Casares, a cave located in the highlands of the Spanish Meseta, where a Neandertal-associated Middle Paleolithic site was discovered and first excavated in the 1960’s. Our main objective is twofold: (1) provide an updated geoarcheological, paleoenvironmental and chronological framework for this site, and (2) discuss obtained results in the context of the time and nature of the last Neandertal presence in Iberia. Methods We conducted new fieldwork in an interior chamber of Los Casares cave named ‘Seno A’. Our methods included micromorphology, sedimentology, radiocarbon dating, Uranium/ Thorium dating, palinology, microfaunal analysis, anthracology, phytolith analysis, archeozoology and lithic technology. Here we present results on site formation processes, paleoenvironment and the chronological setting of the Neandertal occupation at Los Casares cave-Seno A. Results and discussion The sediment sequence reveals a mostly in situ archeological deposit containing evidence of both Neandertal activity and carnivore action in level c, dated to 44,899–42,175 calendar years ago. This occupation occurred during a warm and humid interval of Marine Isotopic Stage 3, probably correlating with Greenland Interstadial 11, representing one of the latest occurrences of Neandertals in the Iberian interior. However, overlying layer b records a deterioration of local environments, thus providing a plausible explanation for the abandonment of the site, and perhaps for the total disappearance of Neandertals of the highlands of inland Iberia during subsequent Greenland Stadials 11 or 10, or even Heinrich Stadial 4. Since layer b provided very few signs of human activity and no reliable chronometric results, and given the scarce chronostratigrapic evidence recorded so far for this period in interior Iberia, this can only be taken as a working hypothesis to be tested with future research. Meanwhile, 42,000 calendar years ago remains the most plausible date for the abandonment of interior Iberia by Neandertals, possibly due to climate deterioration. Currently, a later survival of this human species in Iberia is limited to the southern coasts.