Due to an increase in international demand, quinoa production has boomed tremendously in the Andes since the early 2010s. This has led to significant investments into developing improved varieties for large-scale agribusinesses, but breeding programs are not tailored to the needs of smallholders. In this paper, we study farmers’ preferences and willingness to pay for improved quinoa varieties in the Junín region in Peru. We use data from a choice experiment among 458 smallholders and estimate generalized multinomial logit models to control for preference and scale heterogeneity. We find that farmers generally prefer improved varieties over traditional varieties, with mildew-resistance as the most important crop trait. In general, farmers prefer varieties that are characterized by larger grain sizes, higher yield levels, lower levels of saponin, and a reduced maturation period. Yet, food-insecure farmers are found to be indifferent to early maturity and a larger grain size, which can be explained by a lower degree of commercialization among these farmers. Our results imply that developing mildew-tolerant and higher-yielding varieties with a medium to low saponin content is a priority if investments in quinoa technologies are to benefit small-scale and food insecure farmers in the Andean highlands of Peru.