Watersheds are vital for water regulation, biodiversity conservation, agriculture, and ecosystem services for local and downstream communities. Evaluating traditional Andean land-management practices is therefore crucial for designing sustainable strategies. In this cross-sectional study, we partnered with the Marjuni, Kishuara, and Payanca communities in the Paymakis Agrobiodiversity Zone, located in the Peruvian Andean department of Apurímac. It was analyzed 103 soil samples from continuously cropped fields and Layme fallows of varying durations. It integrated physical and chemical properties into a soil quality index, spatially mapped the results, and complemented them with interviews with 80 farmers on agroecological practices and communal governance. Traditional Laymes fallowing reconfigured soil fertility rather than enhancing all properties uniformly. This fallows generally maintained more favorable acidity, potassium availability, exchangeable nutrients, and nutrient retention. Continuously cropped soils had higher organic carbon but were more acidic and nutrient-depleted. Long-term fallows maintained carbon levels similar to cultivated fields. Although soil quality index values were comparable among management systems, they arose from different combinations of underlying properties. Locally, soil quality was most influenced by texture, acidity, organic carbon, and iron. At the landscape scale, elevation and vegetation were primary structuring factors. Farmers commonly conserved native seeds, avoided chemical inputs, and relied on local knowledge, but structural soil and water conservation practices were limited. These findings highlight the value of community-specific, participatory research that directly links management practices to field-level soil quality, supporting communal governance, ecosystem services, and sustainable management in high-Andean watersheds.