Feeding the world’s population sustainably is a major challenge of our society and has been stated as one of the key priorities for development cooperation by the EU policy framework on food security. However, the current pattern of natural resources exploitation to meet humanity’s demand for food threatens long-term food security. Food systems represent around 30 % of final energy use, generating up to 30 % of greenhouse gas (GHG) emissions. Given the expected increase of global population (9 billion people by 2050) and the amount of food losses and waste generated (a third of global food production), improving the efficiency of food systems along the supply chain is essential to ensure food security. This work combines life cycle assessment (LCA) and data envelopment analysis (DEA) to assess the efficiency of Spanish agri-food system and propose improvement actions in order to reduce energy usage and GHG emissions. Results suggest that sweets and vegetable fats categories provide the largest nutritional energy to consumer per unit of embedded energy in its production. Around a 70 % average reduction target is estimated for the Spanish agri-food system to be efficient, with a similar reduction in related greenhouse gas emissions.