In the High Andes of Bolivia, sectoral fallow systems are a common form of land use. Fields in the study area (Japo, Department of Cochabamba) are cultivated for 3 years with potatoes as the first crop and then lie fallow for 9 years. Despite the low nutrient content of the soil and the high elevation of the area (between 4000 and 4500 m above sea level), farmers achieve relatively high yields. This is explained by traditional knowledge about soil fertility management. The study focuses on nutrient dynamics over a 12-year cycle. A participatory research approach was applied to obtain information about indigenous knowledge. Soil nutrient content, phytomass, and yields were measured in 72 fields together with the farmers. Subterranean phytomass was identified as the key factor in nutrient storage during the fallow period. A multiple linear regression model shows three main factors that determine potato yields on cultivated fields. Farmers know about the nutrient dynamics of the fields; hence, cultivation measures show an impressive rationality. New elements such as mineral fertilizer have been incorporated in the system in a sustainable way. Participatory research intensifies these processes, stimulating farmers to reflect about their own land use system.