This paper presents the results of the archaeological and palaeoenvironmental investigation carried out at Molleres II site located at 2.425 m a.s.l. in the area of Puigpedrós-Malniu (Meranges, La Cerdanya, Eastern Pyrenees). A high-resolution multi-proxy research is proposed combining landscape archaeology, soil micromorphology, anthracology, biomolecular analysis, and radiocarbon dating. This work allowed us to characterize the site's functionality, providing new insight into the occupation dynamics of high mountain spaces starting from the Neolithic onwards. Based on this research Molleres II has been interpreted as a complex and wide open-air site built up by the end of the Middle Neolithic (3636–2701 cal. BC) and consisting of large enclosures entirely dedicated to seasonal animal husbandry and located at an exceptionally high altitude. These unique settings make the site a primer for this period and in the Eastern Pyrenees, revealing the considerable intensity of the animal presence since the Prehistory in these uplands. Following the Neolithic, a second phase of more intense occupation likely occurred during Middle Ages (1179–1434 cal. AD). However, the animal presence in this mountain sector had never been exhausted, even in other historical periods. Palaeoenvironmental data also suggest that such intense and long-term animal presence and possibly fire use could be at the origin of stable grassland-dominated environments and open landscapes maintained almost continuously until nowadays.