Our research addresses the gap in scientific research on the fine-grain spatial patterns and social–ecological interactions of land use and agrobiodiversity. The spatial dimension of agrobiodiversity dynamics potentially strengthens the social–ecological resilience and food security of smallholders by buffering risk and vulnerability. Our research integrates the scientific theories, concepts, and methods of spatial externalities, social–ecological interactions, geospatial land and global change sciences, and political ecology. We designed a case study of the Arbieto-Tarata landscape in the Bolivian Andes that comprises a globally significant agrobiodiversity hot spot of Andean maize. The Arbieto-Tarata landscape, which contains nearly 8000 fields at 2500–2800 masl, is representative of mixed-use smallholder agri-food systems amid global changes. Our research predicts spatial spillover and edge effects of combined social and environmental factors leading to the clustering of same-crop fields. Findings reveal significant levels of the predicted clustering between 2006 and 2012. The degree of this clustering is found to differ among geographic and environmental sub-areas reflecting fine-grain variation of local causal linkages. Extra-local causal linkages include high levels of migration, water resource shortages, and urbanization. Results show the influences of informal and formal coordination in the spatial clustering of same-crop fields. This field-level coordination improves the efficiency of resource allocations and lowers costs of production. It enables the viability of high-agrobiodiversity Andean maize in smallholder land use and agri-food systems amid global changes. The article discusses the broader policy and scientific implications of these findings including scaling up and support of the social–ecological resilience of agrobiodiversity globally.