Molecular and isotopic investigation of lipids from soils filling several structures from an archaeological site located at Obernai (Alsace, NE France) has revealed the presence of miliacin, a triterpenoid marker from Panicum miliaceum (broomcorn millet), indicating that this cereal was cultivated at the site. The concentration profiles of miliacin within silos and its detection in other archaeological structures (e.g., Gaulish pit) suggest that miliacin did not originate from cereals stored in the silos but rather came from remains of millet from cultivated soils which filled the silos after they were abandoned. Furthermore, the 14C age of miliacin isolated from a silo of the Second Iron Age was shown to be considerably older (Bronze Age) than the structure itself, revealing that the soil filling the silo therefore archived the molecular signature from past millet cropping, predating the digging of the silo. Thus, radiocarbon dating of the isolated miliacin allowed the timing of millet cropping to be determined, showing that it was established during the Bronze Age and the Roman Gaul period at Obernai. This is the first evidence of millet cultivation in Alsace dating back to the Bronze Age, bringing new perspectives on agricultural practices and past dietary practice in Eastern France. The combination of molecular studies and radiocarbon dating of individual lipids highlights the potential of hollow structures like silos and pits to act as “pedological traps”, recording information on past vegetation cover or agricultural practices from the surface horizons of surrounding soils that filled these structures after abandonment.