Nutrition, food systems, and the biodiversity of food and agriculture (agrobiodiversity) are rapidly changing among indigenous smallholders in the Andean countries, across Latin America, and globally. Urgent calls for food sovereignty recognize global transformations of nutrition, food systems, agriculture, and climate change amid geographically uneven development and vulnerability to these shocks that recently include the coronavirus/Covid-19 pandemic. Collaborating with a praxis-oriented institution focused on social nutrition and public health in Peru, we conducted mixed-method research on landscape and livelihood transformations among indigenous smallholders in the Huánuco region. Our approach utilizes place- and region-based research that integrates a relational framework of emergent agrobiodiversity interactions with a model of coupling/de-coupling in production-consumption linkages. Conceptual insights and empirical results demonstrate varied but widespread food and nutrition insecurity, moderate agrobiodiversity, and innovative agrobiodiverse maize fields and home gardens. Part-time farming and predominant purchased food are dual pillars amid precarious livelihoods and land use that condition food sovereignty prospects. Cultural affect strongly influences emergent agrobiodiversity utilized in food consumption through relations of gender and intersectional social factors. Global transformations fuel the substantial albeit partial decline of agrobiodiversity. Emergent agrobiodiversity in food-growing spaces can enhance nutrition security and food sovereignty, lessen vulnerability, and strengthen agroecological adaptive capacity and resilience.