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This paper presents the first study that combines the use of ancient crop and animal stable isotopes (carbon and nitrogen) and Zooarchaeology Mass Spectrometry species identification (ZooMS) for reconstructing early farming practices at Kouphovouno, a Middle–Late Neolithic village in southern Greece (c. 5950–4500 cal. BC). Debate surrounding the nature of early farming predominantly revolves around the intensity of crop cultivation: did early farmers move around the landscape while practicing temporary farming methods such as slash and burn agriculture or did they create more permanent fields by investing high labor inputs into smaller pieces of land that produced higher crop yields? The need to address these questions using a direct assessment of the intensity and scale of cultivation is apparent, and an integrated stable isotope approach provides such an opportunity. The results of this study support the model of small-scale mixed farming, where crop cultivation and animal husbandry are closely integrated. The farmers directed their intensive management towards crops grown for human consumption (free-threshing wheat), while growing fodder crop (hulled barley) more extensively. Pulses were cultivated under a high-manuring/high-watering regime, likely in garden plots in rotation with free-threshing wheat. The diets of the livestock enable us to investigate which parts of the landscape were used for browsing and grazing and indicate that animal management changed in the Late Neolithic. The sheep and goats were now kept in smaller numbers and grazed together and new pasture grasses may have been sought for the grazing of cattle. This study demonstrates that beyond its applicability for palaeodietary reconstruction, analysis of stable isotopes of archaeological crop and animal remains has important implications for understanding the relationship between humans, plants and animals in an archaeological context.