Our research occurred in the Andean region, one of the eight global centers of domestication of plant species grown for agriculture. The shores of Lake Titicaca (located between Peru and Bolivia), at 3800 meters above sea level, are recognized as the center of origin of quinoa (Chenopodium quinoa Willd.). In this region, complex societies have emerged, thanks to the development of water and soil management technologies. They have managed to overcome high mountain territories’ extreme and variable climatic conditions. These societies have traditionally protected and preserved quinoa as food for present and future generations through their long-standing knowledge and cultivation practices. The fieldwork occurred in the context of Andean family farming, and our study analyzes nature-society dynamics with a chorematic approach and interviews with local communities. The interest of this work is the transformation of the landscape at the scale of the mountain agroecosystem to understand better the impacts of rural development policies. Chorematic modeling was applied to two periods, before and after 1970, a pivotal year in Peru for agriculture, to show how socio-spatial dynamics in the Andean environment are changing, particularly concerning the evolution of quinoa cultivation. The results show that wild quinoa relatives’ distribution is strongly linked to the socio-spatial organization of the agroecosystem. Different species of wild quinoa relatives are maintained by villagers for their multiple foods, medicinal and cultural uses in natural areas, grazed areas, on edge, and also within cultivated fields. However, this management is changing under the pressure of global issues related to the international quinoa market, whose requirements imply reducing the presence of wild relatives in cultivated fields.