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Smallholder farmers are some of the poorest and most food insecure people on Earth. Their high nutritional and economic reliance on home-grown produce makes them particularly vulnerable to environmental stressors such as pollinator loss or climate change which threaten agricultural productivity. Improving smallholder agriculture in a way that is environmentally sustainable and resilient to climate change is a key challenge of the 21st century. Ecological intensification, whereby ecosystem services are managed to increase agricultural productivity, is a promising solution for smallholders. However, smallholder farms are complex socio-ecological systems with a range of social, ecological and environmental factors interacting to influence ecosystem service provisioning. To truly understand the functioning of a smallholder farm and identify the most effective management options to support household food and nutrition security, a holistic, systems-based understanding is required. In this paper, we propose a network approach to understand, visualise and model the complex interactions occurring among wild species, crops and people on smallholder farms. Specifically, we demonstrate how networks may be used to (a) identify wild species with a key role in supporting, delivering or increasing the resilience of an ecosystem service; (b) quantify the value of an ecosystem service in a way that is relevant to the food and nutrition security of smallholders; and (c) understand the social interactions that influence the management of shared ecosystem services. Using a case study based on data from rural Nepal, we demonstrate how this framework can be used to connect wild plants, pollinators and crops to key nutrients consumed by humans. This allows us to quantify the nutritional value of an ecosystem service and identify the wild plants and pollinators involved in its provision, as well as providing a framework to predict the effects of environmental change on human nutrition. Our framework identifies mechanistic links between ecosystem services and the nutrients consumed by smallholder farmers and highlights social factors that may influence the management of these services. Applying this framework to smallholder farms in a range of socio-ecological contexts may provide new, sustainable and equitable solutions to smallholder food and nutrition security. A free Plain Language Summary can be found within the Supporting Information of this article.