Investigating pottery function requires optimal preservation of both ceramic vessels and organic residues related to vessel use. If these criteria are met then opportunities emerge for combining macroscopic observations, typological classification, and capacity measurements and molecular and isotopic proxies (GC, GC-MS, and GC-C-IRMS) to explore vessel use and resource exploitation. The exceptional ceramic assemblage of hundreds of vessels excavated from the Middle Neolithic site of Clairvaux XIV (Jura, France, IVth millennium B.C.) offered such an opportunity, with a wide diversity of vessel shapes and extraordinary preservation of lipids. Interrogating the lipid residues together with typological analyses revealed a complex system of ceramic vessel use. Despite the scarcity of aquatic products, a wide diversity of natural substances has been detected: ruminant adipose fats, dairy products, plant substances, and beeswax. These commodities were processed in specific vessels with three main different functions: cooking vessels of various volumes, serving dishes for animal products, and dedicated vessels for dairy product processing and consumption.