During the Bronze and Iron Age, Sardinia was home of one of the most technologically advanced Mediterranean societies (the Nuragic culture). Given its key geographical location, the island was also the fulcrum of deep cultural exchanges. Toward the end of the Iron Age, Phoenicians, and especially Carthaginians and Romans, massively frequented Sardinia for different purposes. This marks an important cultural transition for the region, as the ancient Nuragic-related society terminated. At the same time, this impacted the subsistence and land use practices. Together with middle to late Holocene climate changes, the novel anthropic activities had a pivotal role in shaping the landscape around the island. However, high resolution climate and environmental records for these culturally important phases are still lacking in Sardinia. Thus, this paper explores palaeoenvironmental changes from the Bronze Age to post Iron Ages times by using carbonate speleothems from Suttaterra de Sarpis Cave (Urzulei, central east Sardinia), strategically located nearby the Or Murales Nuragic Village. U–Th ages (n = 20) indicate that five stalagmites comprehensively span the last ∼7000 years. Peculiarly, they all show an evident stratigraphic discontinuity. Age models attest that hiatuses can be at times associated with the discontinuities, spanning periods of ∼1200 to ∼200 years. Importantly, the discontinuities occurred from the Late Iron Age to the Roman period. Based on fabric observations, trace elements and δ13C- δ18O analyses, the discontinuities are primarily attributed to a progressive change of land use above the cave. We suppose that deforestation aimed to clearance for agriculture and livestock practices probably was the most impacting factor for infiltration dynamics and soil state, thus affecting the studied speleothems, although archaeological and historical data are absent for the specific study area. Instead, this is in line with the cultural transition occurring in Sardinia toward the end of the Iron Age, with novel agricultural practices imported by the overseas populations. The anthropic disturbance to the millennial-long karst equilibrium possibly overprinted the response of speleothem proxies to climate oscillations, although future higher resolution analyses are necessary to better investigate the evolution of climate during the Holocene as well as its role in the development of ancient civilizations. Indeed, this is the first speleothem-based Holocene palaeoenvironmental reconstruction accomplished in Sardinia. Considering the paucity of natural lakes in this key location, speleothems here demonstrate their potential in exploring human-driven palaeoenvironmental changes during times of cultural transitions within the Mediterranean context.