Systems and methods are provided for incorporating molten carbonate fuel cells into a heat recovery steam generation system (HRSG) for production of electrical power while also reducing or minimizing the amount of CO2 present in the flue gas exiting the HRSG. An optionally multi-layer screen or wall of molten carbonate fuel cells can be inserted into the HRSG so that the screen of molten carbonate fuel cells substantially fills the cross-sectional area. By using the walls of the HRSG and the screen of molten carbonate fuel cells to form a cathode input manifold, the overall amount of duct or flow passages associated with the MCFCs can be reduced.