Systems and methods are provided for capturing CO2 from a combustion source using molten carbonate fuel cells (MCFCs). At least a portion of the anode exhaust can be recycled for use as a fuel for the combustion source. Optionally, a second portion of the anode exhaust can be recycled for use as part of an anode input stream. This can allow for a reduction in the amount of fuel cell area required for separating CO2 from the combustion source exhaust and/or modifications in how the fuel cells can be operated.