The search for sustainability in energy systems has increased the concern to reduce pollutant emissions and waste. Among the several strategies that help in this task are increased energy efficiency, carbon capture and storage, hybrid renewable-fossil systems, and system integration. All of them often result in complex multi-fuel multi-product systems. Conventional thermoeconomic analysis of such systems does not give information related to the type of energy source used, nor to the emissions generated. The aim of this work is to provide a method to reveal the fate of energy resources inside a system. We present a methodology to decompose exergy flows into as many parts as different types of external resources a system has. The proposed method was applied to a cogeneration system, showing to be a powerful tool to analyze multi-fuel systems, especially hybrid fossil-renewable plants, since the evolution of fossil resources can be tracked through the entire system. It also presents an answer to the unsolved problem of discriminated conversion efficiency, fuel impact and CO2 emissions impact when different fuels are used, which allows an extended analysis of energy systems, by taking into account the existence of a carbon tax. (C) 2013 Elsevier Ltd. All rights reserved.