Over the last century we have seen an unprecedented growth in both global food production and associated socio-environmental conflicts, connected to increasingly industrialized farm systems and a decline in biodiversity. The objective of this presentation is to bring together an integrated methodology, applicable to different spatial scales (from regional to local), to deal with the long-term socio-metabolic balances and changes in the ecological functionality of farm systems. We propose an Intermediate Disturbance-Complexity model of agroecosystems (Marull et al. 2016a) to assess how different levels of human appropriation of photosynthetic production affect the functional landscape structure that hosts biodiversity on a regional scale. We have developed an Energy-Landscape Integrated Analysis (Marull et al. 2016b) that allows us to measure both the energy storage represented by the complexity of internal energy loops, and the energy information held in the whole network of socio-metabolic energy flows in order to correlate both with the energy imprint in the landscape patterns and processes that sustain biodiversity on a local scale. Further research could help to reveal how and why different management strategies of agroecosystems lead to key turning-points in the relationship between energy flows, landscape functioning and biodiversity. There is no doubt that this research will be very useful in the future to help design more worldwide sustainable food systems.