Human land use changes have altered soil erosion for millennia with extensive consequences on terrestrial and aquatic ecosystems as well as on biogeochemical cycles along the land-ocean continuum. Despite their great importance, past erosion trends have high uncertainties limiting quantitative estimates of long-term erosion dynamics. Here, we applied a new approach combining well-dated paleo-records of soil erosion from lake sediments and a spatially distributed semi-empirical model to simulate annual soil erosion in six lake watershed systems in the Northwestern Alps during the Holocene. Progressive and abrupt changes in soil erosion are detected in the six watersheds. Progressive erosion explains most of the soil exports observed during the Early to Mid-Holocene period (from 11,700 to 3000 cal. yr. BP), while transient erosion crises (i.e., periods of abrupt increase in the erosion rates spanning approximately 1000 ± 500 years) led to massive soil losses during the Late-Holocene period (from 3000 to 1000 cal. yr. BP). Our coupled approach of proxy-model reconstruction shows that the transient erosion crises represent the half of the total soil erosion exports during the Holocene. These estimates defy current representations of large-scale soil erosion during the Holocene that do not consider transient erosion crises, hence potentially underestimating the anthropogenic perturbation of lateral fluxes and fate along the land-ocean continuum. Our results further suggest that erosion and/or land cover proxies need to be consistently integrated into model approaches when attempting to estimate past variations in mass exports from terrestrial to aquatic ecosystems over centennial to millennial timescales.