Background: To achieve a healthy sustainable food system globally, it is imperative to understand how local food systems can provide healthy and sustainable conditions. Objective: To explore, through the indigenous community of Caliata in the Ecuadorian highlands, the factors that support or hinder sustainable Andean food systems. Methods: We designed a participatory mixed-methods study in Caliata (Chimborazo, Ecuador) and an inclusive and transdisciplinary research process with constant member checking. The study combined culturally validated qualitative methods (n = 49), agroecology-based site analysis, and household surveys (n = 57), including a modified 48-h recall. We used the NOVA food classification system to categorize the diet according to levels of processing and analyzed categorical and numeric data to understand the interplay of parcel size, agrodiversity, and diet diversity. Results: First, the agroecological space is defined by the stewardship of Pachamama (Mother Nature), a central role in Andean cosmovision, leading to trophic interactions and cycles characterized by a diversity of heterarchical social organizations and agroecologically useful species. Second, consistency was found in dietary patterns; all respondents consume their produce, fruits being the most popular snack (in a 24-h period, 70% reported an average of 2.2 servings), and two-thirds of households' consumption represent unprocessed or minimally processed foods. Third, gendered agriculture and population aging represent demographic challenges, while chronic health problems remain relatively infrequent compared with the general population. Fourth, food sovereignty is an ecocentric concept based on production, exchanges of seeds and produce, consumption of produce, and knowledge of how agroecological space is treated. This system represents a nutrient loop tied to a system of knowledge about how to care for soil, land, and the ecological community. Conclusions: Caliata provides important perspectives on linkages between diet, biodiversity, use of agroecological space, and rural-urban dynamics. This small indigenous community offers lessons for achieving both healthy ecosystems and food security.