In spite of its slow commercial deployment, fuel cells are amongst the most efficient and environmentally friendly electric power generators. The case of Molten Carbonate Fuel Cells is even more interesting since, in addition to these features that are common to all fuel cells, these systems can be used as active carbon capture devices due to their capability to migrate carbon dioxide from one electrode (cathode) to another (anode). In this context, this work presents the operation of a fuel cell of this type coupled to a combined heat and power plant based on gas reciprocating engines as typically used in wastewater treatment plants. The biogas produced in the water sludge digestion process is burnt in the reciprocating engines, whose exhaust gases are mixed with air and blown into the fuel cell cathode. The carbon dioxide contained in this stream is conveyed in the form of carbonate ions (CO3=) through the electrolyte to the anode where it reacts with the hydrogen fuel, being released as carbon dioxide. The exhaust gases from the anode comprise carbon dioxide, water steam and a small fraction of unspent hydrogen fuel. The combustion of the latter species with pure oxygen followed by a cooling process permits separating a gaseous stream of pure carbon dioxide from a liquid stream of water. The interest of this carbon sequestration system is twofold. On one hand this system captures CO2 and, at the same time, generates electricity as opposed to conventional systems based on amines or other sorbents which exhibit high power consumption. On the other hand, the avoided CO2 can be traded in a potential carbon trading system. Nevertheless, in spite of the undisputable thermodynamic and environmental benefits, the very high capital cost of the fuel cell might bring about a lack of economic interest in comparison with the standard reference plant using gas engines only. Thus, this paper reviews different configuration based on fuel cells and provides an interesting economic assessment with respect to these novel proposals. More in particular, it is shown that using fuel cells is not economically attractive presently given the low commercial maturity of these devices though, in a near future where higher technology readiness levels are expected, a definite advantage over conventional facilities is envisaged. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.