El Niño cave, located on the south-eastern border of the Spanish Meseta, hosts a discontinuous sequence including Middle Palaeolithic and Neolithic levels, along with Upper Palaeolithic and Levantine style paintings. It is a key site for understanding human occupations of inland Iberia during the Palaeolithic and early prehistory. This paper summarises the main results of a multidisciplinary project aimed at defining the prehistoric human occupations at the site.