In order to better understand the evolution of past climate-human-environment interactions in the North-western Alps during the Holocene, we have analysed the lipid content of two cores taken from the sediments of Lake le Bourget (French Alps). By using a specific molecular biomarker of Panicum miliaceum (broomcorn millet) previously defined and a new molecular marker of soil erosion, we demonstrate that the onset of millet cultivation coincides with the onset of major soils erosion in the catchment during the Middle Bronze Age. Although archaeological and archaeobotanical investigations indicate a discrete human occupation of the lakeshores at this period, they also point to a regional change in agricultural practices that deeply affected soils. The evolution of millet cultivation appears in strong connection with climatic variations, estimated in the same cores from the variations in titanium, a proxy of hydrological changes in the region. Social and cultural triggers cannot be discarded at this stage. Such an approach applied to more sedimentary archives shows high potential to unravel the temporal and spatial dynamics of human land-use.