The Late Neolithic and Chalcolithic periods are poorly understood in northeastern Iberia. Most of the information comes from the sepulchral structures rather than habitat settlements. The high number of individuals usually recovered from this types of collective burial spaces, together with the low number of direct radiocarbon dates available on them, forces us to be cautious and consider all the studied assemblages as belonging to the so-called Late Neolithic-Chalcolithic time period. To evaluate human dietary patterns of the Late Neolithic-Chalcolithic populations from the northeast of Iberia, stable carbon and nitrogen isotope analysis was carried out on 78 humans and 32 faunal bones from Cova de laGuineu (Font-rubí, Barcelona) and Cueva de Abauntz (Arraitz, Navarra), both of them sepulchral sites. Results show a common dietary pattern in both sites, indicating an homogeneous protein diet based on C3 terrestrial resources and no isotopic evidence of the consumption of C4 plants. Only one individual from Cueva de Abauntz, who directly dates to the first moments of the use of the cave as a burial place, suggests a different protein intake. The inter-population analysis shows a significant difference between both human and faunal δ13C values, suggesting an environmental influence on the isotope values depending on the geographic location. This effect should not be discarded and always assessed with baseline isotopic values in future studies at each area of Iberia and for different chronological moments.