Solid oxide fuel cell–gas turbine (SOFC‐GT) systems provide a thermodynamically high efficiency alternative for power generation from biofuels. In this study biofuels namely methane, ethanol, methanol, hydrogen, and ammonia are evaluated exergetically with respect to their performance at system level and in system components like heat exchangers, fuel cell, gas turbine, combustor, compressor, and the stack. Further, the fuel cell losses are investigated in detail with respect to their dependence on operating parameters such as fuel utilization, Nernst voltage, etc. as well as fuel specific parameters like heat effects. It is found that the heat effects play a major role in setting up the flows in the system and hence, power levels attained in individual components. The per pass fuel utilization dictates the efficiency of the fuel cell itself, but the system efficiency is not entirely dependent on fuel cell efficiency alone, but depends on the split between the fuel cell and gas turbine powers which in turn depends highly on the nature of the fuel and its chemistry. Counter intuitively it is found that with recycle, the fuel cell efficiency of methane is less than that of hydrogen but the system efficiency of methane is higher.