Scientific and policy interest in the biological diversity of agriculture (agrobiodiversity) is expanding amid global socioeconomic and environmental changes and sustainability interests. The majority of global agrobiodiversity is produced in smallholder food-growing. We use meta-analyses in an integrated framework to examine the interactions of smallholder agrobiodiversity with: (1) livelihood processes, especially migration, including impacts on agrobiodiversity as well as the interconnected resource systems of soil, water, and uncultivated habitats; and (2) plant–soil ecological systems. We hypothesise that these interactions depend on: (1) the scope of livelihood diversification and the type of resource system; and (2) plant residues and the aboveground/belowground component of ecological specificity. Our findings show: (1) livelihood diversification is linked to varied environmental factors that range from rampant degradation to enhanced sustainability; and (2) there is significant ecological coupling of aboveground and soil agrobiodiversity. The environmental impacts of livelihood interactions correspond to the variation of diversification (migration, on-farm diversification) and resource system (i.e. agrobiodiversity per se, soil, water). Our findings also reveal mutually dependent interactions of aboveground and soil agrobiodiversity. Results identify livelihood diversification-induced reduction of environmental resource quality with lagged agrobiodiversity declines as a potentially major avenue of global change. Our contribution re-frames livelihood interactions to include both agrobiodiversity and ecological systems. We discuss this integrated social–environmental re-framing through the proposed spatial geographic schema of regional agri-food spaces with distinctive matrices of livelihood strategies and relations to biodiversity and resources. This re-framing can be used to integrate livelihood, agrobiodiversity and ecological analysis and to guide policy and scientific approaches for sustainability in agriculture and food-growing.