During the last decade there was a great growth in biofuel industry and commercial bioenergy use all over the world. The last few years this tendency suffered drawbacks due to new rules and pressure over the public questioning the sustainability of biofuels and their capability to achieve environmental and social solutions. Arguments came from, energy balances, carbon and more recently water impacts. Public perception can be changed very rapidly in modern societies with plenty of media roads to reach people quikly. Different actors as oil and food companies, NGO, environmentalist publish certain reports of big impact in the general public. When the perception is changed political actors try to respond promoting new legislation, laws and commerce regulations. In general, report results are based on future forecast figures of impacts because of using world equilibrium econometric models. Many studies are incomplete lacking a systemic and holistic view of biofuels within agriculture markets all over the world. The industry is suffering this continuous drawbacks working at a low rate or closing. From an analysis of the principal biofuels markets in the world with an increasing role on the last years, we find out that they are all inserted in complex agro industrial transforming chains with several products being produced and commercialized at the same time and from common feedstock. In this paper, a systemic approach proposal is developed looking for real impact of this industry within very complex markets were co-products and flex crops are a key factor. Analysis on traceable and public figures comparing them with forecast and projections made by equilibrium models all over the word are described. Results are based on a complete transformation chain analysis of Argentina case as the first biodiesel exporter country until 2012 and one of the main actors in agricultural commodity markets. Preliminary results confirm that forecast consequences are very far from real markets and land use behavior. Carbon emitions and water impacts of first and second-generation biofuels need to be revised and closely look at in order to compare them in a fair way. There is also an urgent need to increase transparency regarding methodologies, frontiers and allocation rules followed in bioenergy and biofuel studies. ISO 14040/44/25 standards give a good starting point and future studies should follow their technical guidance in order to make appropriate comparisons over the base of environmental product declarations (EPD).