Fertilization is one of the agronomic practices that generates the highest environmental burdens in energy crops. However, this practice is essential, since its omission could entail long term processes of soil degradation, endangering the environmental sustainability of agricultural systems. In most of the Life Cycle Assessment (LCA) of energy crops found in the scientific literature, the inputs and outputs of nutrients are not calculated and the environmental impacts of nutrient loss are ignored as well. In this paper, a methodological approach to calculate the balance of nutrients that occurs during annual crop production in the context of the Life Cycle Inventory phase of LCA is proposed and applied to two study cases of energy crops: rapeseed (Brassica napus) in Cadiz, Spain, and soybean (Glycine max) in Buenos Aires, Argentina. The results show that when rational fertilization is carried out, rapeseed fertilization in Spain generates more severe environmental impacts than soybean in the Argentinean Pampas when 1 ha of crop per year is used as the functional unit. (C) 2013 Elsevier Ltd. All rights reserved.