According to the agroecological approach, energy analyses applied to agriculture should provide information about the structure and functions of the agroecosystem; in other words, about the maintenance of its fund elements, which sustain the flow of ecosystem services. To this end, we have employed a methodological proposal that adds agroecological EROIs to the existing economic EROIs. This methodology is applied here for the first time at the country level, and over a long-term historical period. The Spanish agroforestry sector, which is representative of Mediterranean agroclimatic conditions, has been studied on a decadal basis from 1900 to 2008, fully spanning its process of industrialization and modernization. The results show the loss of energy efficiency brought about by the industrialization of Spanish agriculture. The economic EROIs (FEROI, EFEROI and IFEROI) fell by 42, 93 and 12%, respectively. The shift towards livestock production and the dramatic increase in industrial inputs are the causes of this decline. With regard to agroecological EROIs, NPPact EROI and Biodiversity EROI fell by 6 and 15%, respectively. This suggests that the fund elements are being degraded and alerts us to low returns to nature in the form of un-harvested biomass available to aboveground and underground wildlife. Finally, Woodening EROI increased by 48%. Sixty percentage of this increment was due to the growth of woodland in areas freed from agricultural activities. However, this change in land use was partly due to feed imports from third countries where deforestation processes may well be taking place, an effect that has not been considered in the analysis.