The Alsace region bordering the Rhine River was extensively occupied during the Neolithic by farming societies with domesticated animal. The first settlers were two sub-groups of the Linearbandkeramik who appeared to diverge in several respects, including: pottery styles, house orientations and funerary rituals. To explore whether this was reflected in food procurement practices investigations were performed of organic residues in nearly 900 pottery vessels from sites across the region. The results reveal lipid biomarker and stable carbon evidence for exploitation of plant and bee products, and most significantly, extensive domestic animal products including: non-ruminant carcass products, and ruminant primary and secondary products. Critically, culturally-related economic differences were seen spatially between the upper and lower Alsatian groups. Temporal differences were confirmed using compound-specific radiocarbon dating of fatty acids preserved in potsherds, showing that while milk exploitation was widespread during the early Neolithic in UA, it only became commonplace in LA generations later.