This paper is aimed at presenting a methodology for the simultaneous synthesis of solid oxide fuel cell (SOFC) based systems and their associated heat exchangers network (HEN). The optimization model is formulated as a mixed integer nonlinear mathematical programming (MINLP) problem. The optimization goal is to maximize the overall net efficiency of the integrated system. Ethanol and glycerin are studied as fuels fed to the SOFC system as they constitute two renewable and sustainable sources of energy. As main results, net global efficiency values of 69.35% and 66.97% were computed for ethanol and glycerin, respectively. For both cases, the computed optimal operation pressure, the SOFC operation temperature and the fed water/fuel molar ratio values were 2 atm, 1073 K and 3, respectively. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.