Semi-domesticated plants are good resources for agroecology, because they can survive without human intervention and can be managed together with non-domesticated plants. To explore the ecological know-how underlying farmer management of semi-domesticates at the landscape level, we compared how Yanacona Indigenous People in the southwestern Colombian Andes manage two semi-domesticated species of Phaseolus beans, both locally named cacha (Phaseolus coccineus and P. dumosus), and a full domesticate (the common bean Phaseolus vulgaris). We investigated what functional traits of Phaseolus beans farmers identify and how farmers link these traits with the ability of beans to develop in different cultural-ecological niches within the landscape. In 60 semi-structured interviews conducted with Yanacona farmers, we found that (i) farmers compare functional traits of the different bean species, including perenniality, phenology, resistance to pests and diseases, and ability to compete with surrounding vegetation; (ii) farmers recognize and use the variation generated by hybridization between the two cacha species; (iii) farmers take advantage of the traits of cacha to grow them under a wide array of niches at the landscape scale, including low-intervention spaces, such as hedges and swidden plots in fallow, and have detailed knowledge of cacha beans' interactions with trees; and (iv) cacha traits contribute to the resilience of agroecosystems through the management practices and social relationships with which they are associated. Emic and etic perspectives must be combined to gain full understanding of the roles of functional traits of cultivated plants.