In various aspects, systems and methods are provided for integrating molten carbonate fuel cells with a fired heater for production of electrical power while also reducing or minimizing the amount of CO2 present in the flue gas generated by the fired heater. The molten carbonate fuel cells can be integrated for use with fired heater so that at least a portion of the flue gas from fired heater flows through cathodes of the fuel cells and at least a portion of the cathode exhaust is returned to a convection section of the fired heater.