In the last five years or so, biofuels have been given notable consideration worldwide as an alternative to fossil fuels, due to their potential to reduce greenhouse gas emissions by partial replacement of oil as a transport fuel. The production of biofuels using a sustainable approach, should consider local production of biofuels, obtained from local feedstocks and adapted to the socio-economical and environmental characteristics of the particular region where they are developed. Thus, decentralized energy from waste systems will exploit local biomass to optimize their production and consumption. Waste streams such as agricultural and wood residues, municipal solid waste, vegetable oils, and algae residues can all be integrated in energy from waste systems. An integral optimization of decentralized energy from waste systems should not be based on the optimization of each single process, but the overall optimization of the whole process. This is by obtaining optimal energy and environmental benefits, as well as collateral beneficial co-products such as soil fertilizers which will result in a higher food crop production and carbon dioxide fixation which will abate climate change.