The intensification of crop production is widely recognized to negatively affect the agrobiodiversity in smallholder systems. This trend can also be observed in Quinoa production systems, where few varieties are commercialized while maintaining traditional varieties of quinoa remains a key agricultural activity in the high-Andes landscape. In recent decades, the “boom” of quinoa production has given rise to national projects intended to ensure that farmers benefit from their agricultural heritage, including the development of a collective trademark. However, little is known about the opinions of smallholder farmers regarding quinoa varieties cultivation, farming practices, market choices, or the development of a collective trademark as a tool to safeguard a position in the booming international quinoa market. To address these questions, we developed our research in three villages in the Puno region of Peru, quinoa's center of origin. We applied a novel combination of participatory methods: the Q methodology to interpret the perceptions of smallholder quinoa farmers concerning the activities that are important on their farms, and the Four-Square Analysis workshops to explore quinoa biodiversity management. The results of our Q-analysis revealed three types of opinions emerging among farmers: (Type 1) Conservationist, (Type 2) Intensification sustainer, and (Type 3) Collaboration seeker. Type 1 assigns importance to maintaining and promoting quinoa biodiversity through collective practices and markets. Type 2 focuses on developing export-oriented production based on certified and improved varieties, combined with efficient ways of storing quinoa. Type 3 appears to value the collective aspects of organizations and cooperation among stakeholders. According to the results of the Four-Square Analysis, most landraces of quinoa are threatened by genetic erosion, as they are cultivated in situ in small plots and on few farms. Our results are an important baseline for further project development for biodiversity conservation in situ and market inclusion engaging local communities.