With the arrival of the Neolithic to Europe, new ways of life and new subsistence strategies emerged. In the Paris Basin (northern France), the appearance of some monumental funerary structures during the Middle Neolithic highlights in particular the increasing complexity of the social organisation. At the same time, several sites, such as open-air cemeteries, do not display any evidence of such arrangement. In the southeast of this area, the two primary routes of neolithisation meet. Several funerary parameters attest to the diverse influence received from other surrounding cultures. In order to assess potential differences in diet, and therefore on purported social distinctions at the inter- and intra-site level, stable isotope analyses (carbon, nitrogen and sulphur) were performed on bone collagen of humans (n = 177) and non-human animals (n = 62) from seven archaeological sites located in the same area (< 10 km). This study is the biggest so far on French Neolithic material and thus allows for an extensive investigation at a regional scale. Results show that the human nitrogen isotopic ratios are relatively enriched in nitrogen-15 comparing to those of the domesticated animals. This reflects a trophic step that is rarely observed elsewhere in the surrounding Neolithic people, particularly for humans of the biggest site Gurgy “Les Noisats”. Though zooarchaeological data support a predominant cattle consumption, here, we propose a mixed protein consumption of cattle and pig, possibly complemented with some freshwater resources. Furthermore, carbon, nitrogen and sulphur isotopic ratios suggest some slight differences between sexes and sites. This sexual distinction has rarely been identified in the diet within a Neolithic context. Some variations over time were also detected. On the whole, this study seems to support previous observations made from burial practices about a specific regional Neolithic pattern in the Paris Basin as well as bring new elements into discussion of social organisation in human populations.