The emergence of agriculture during the Formative period in the southern Lake Titicaca Basin played a crucial role in the development of the region’s first complex societies. Our study of Chenopodium seeds from the site of Chiripa, Bolivia, sheds light on some of the small-scale processes contributing to the development of agricultural systems between 1500 B.C. and A.D. 100. Using a combination of scanning electron and light microscopy, we identified the crop/weed complex of the domesticate, quinoa (C. quinoa Willd.), and its weedy relative, quinoa negra (C. quinoa var. melanospermum Hunziker), at Chiripa by 1500 B.C. Analyses of quinoa/quinoa negra morphometry and seed frequencies suggest that during the Early Formative period, farmers maintained gardens where both the crop and weed grew and were harvested for consumption. Around 800 B.C., however, we find samples almost entirely of quinoa at Chiripa’s social and political center, the Montículo. The paucity of quinoa negra seeds suggests that Middle Formative period farmers became more meticulous cultivators of quinoa, perhaps through weeding, careful seed selection, and construction of fields. This study complements previous investigations of settlement patterns, landscape modification, and stone tool use in this region, providing a richer understanding of Formative period agriculture.