Energy balances of farm systems have overlooked the role of energy flows that remain within agro-ecosystems. Yet, such internal flows fulfil important socio-ecological functions, including maintenance of farmers themselves and agro-ecosystem structures. Farming can either give rise to complex landscapes that favour associated biodiversity, or the opposite. This variability can be understood by assessing several types of Energy Returns on Investment (EROI). Applying these measures to a farm system in Catalonia, Spain in 1860 and in 1999, reveals the expected decrease in the ratio of final energy output to total and external inputs. The transition from solar-based to a fossil fuel based agro-ecosystem was further accompanied by an increase in the ratio of final energy output to biomass reused, as well as an absolute increase of Unharvested Phytomass grown in derelict forestland. The study reveals an apparent link between reuse of biomass and the decrease of landscape heterogeneity along with its associated biodiversity.