Centuries of cultivation in the Highland Aynoka of Puno, Peru, have endowed indigenous crops such as potato and quinoa with rich cultural and nutritional value deeply ingrained in local traditions. This study meticulously evaluates their economic viability, environmental implications, and cultural importance by employing a mixed-methods research approach involving surveys, interviews, and observations. The outcome reveals that while the Economic Sustainability Index (EKI) moderately supports potato and quinoa production sustainability, with a value of 2.98, it falls short of significant impact. Conversely, the Environmental Sustainability Index (ESI) and the Social Sustainability Index (SSI) exhibit moderate levels of sustainability, recording values of 4.04 and 3.38 for ESI and SSI, respectively. These crops demonstrate acceptable economic feasibility, marked by consistent sales, income generation, and manageable production expenses. The findings underscore the urgency of endorsing sustainable farming methods to safeguard cultural heritage, boost market prospects, and fortify regional ecological robustness. Rooted in ancestral sustainability, potato and quinoa cultivation is a cornerstone in local food systems. Recognizing the cultural, economic, and environmental significance inherent to these crops, efforts can be channeled towards nurturing sustainable agricultural systems that uphold community well-being, conserve biodiversity, and facilitate cultural resilience in Puno’s Highland Aynoka.