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Archaeobotanical investigations of the Early Neolithic settlement of Fondo Azzollini (Molfetta, SE Italy) have been carried out since 1999 in order to reconstruct the environmental changes that occurred in the Murgia region (Puglia) during the main occupation phases of the site. The archaeological site is located on a calcareous plateau sloping down to a sinkhole called “the Pulo”. The rock surfaces of the sinkhole are marked by several caves, inhabited also during the Bronze Age. The heavy erosion processes active in the settlement area and the distinctive morphology of the plateau have caused eroded sediments to flow into the adjacent natural basin. This study compares archaeobotanical remains from the archaeological site (in-site data) and plant remains from the S1-bis core drilled in the Pulo (off-site data). AMS radiocarbon dating indicated that the lowest part of the S1-bis core had the same age as the Neolithic settlement, whereas the upper part of the core corresponded to the Bronze Age habitation of the caves. The off-site plant remains found in the core enriched the rather scarce archaeobotanical data from the archaeological site itself and enabled us to identify changes in plant resources and cultivation practices.