Soils have a substantial role in the environment because they provide several ecosystem services such as food supply or carbon storage. Agricultural practices can modify soil properties and soil evolution processes, hence threatening these services. These modifications are poorly studied, and the resilience/adaptation times of soils to disruptions are unknown. Here, we study the evolution of pedogenetic processes and soil evolution phases (progressive or regressive) in response to human-induced erosion from a 4000-year lake sediment sequence (Lake La Thuile, French Alps). Erosion in this small lake catchment in the montane area is quantified from the terrigenous sediments that were trapped in the lake and compared to the soil formation rate. To access this quantification, soil processes evolution are deciphered from soil and sediment geochemistry comparison. Over the last 4000 years, first impacts on soils are recorded at approximately 1600 yr cal. BP, with the erosion of surface horizons exceeding 10 t·km− 2·yr− 1. Increasingly deep horizons were eroded with erosion accentuation during the Higher Middle Ages (1400–850 yr cal. BP), reaching 1000 t·km− 2·yr− 1, and leading to the remobilization of carbonated and poorly weathered material, hence rejuvenating soil development. Erosion exceeded the soil formation rate and constituted a regression in the development of soils. The tolerable erosion limit is thus defined for erosion from 25 to 30 t·km− 2·yr− 1. Beyond this limit, the sustainability of the agroecosystem is limited and ecosystem services decrease. Afterwards, pedogenesis evolved again from progressive (700–300 yr cal. BP) to regressive (300 yr cal. BP-today) phases. Erosion was less important during the last 700 years than during the Middle Ages but with the same weathering stages, indicating that soils were deeply affected during the Middle-Age and have yet not recovered. Our results highlight the importance of the human factor in the pedogenesis over last millennia and suggest that the studied agro-ecosystem entered the Anthropocene 1400 years ago.