Reducing the global carbon footprint is imperative in the light of increasing climate pressures. Replacing fossil fuels with renewable or waste-derived fuels is the long-term goal. Capturing and sequestering anthropogenic carbon dioxide (CO2) emissions, the so-called carbon capture and sequestration (CCS) process, is an intermediate step until that transition can be accomplished. EU-funded scientists working on the project MCFC-CONTEX are optimising exploitation of molten–carbonate fuel cells (MCFCs) for this purpose. MCFCs can extract CO2 from power plant flue gas on the cathode side and convert sustainable hydrocarbon fuels such as biogas into electricity on the anode side. Thus, they can be used in a wastewater treatment plant as an MCFC CHP generator fed with biogas from the treatment process. Contaminants in non-conventional fuels of organic (waste-derived) origin cause degradation in MCFC performance and researchers are addressing this barrier. They are investigating poisoning mechanisms to determine MCFC tolerance limits for long-term performance and reliability. Simultaneously, they are also optimising clean-up of biogas from wastewater treatment and natural gas to ensure that purification levels are in line with the MCFC tolerances. Scientists began by determining the relevance and priority of selected contaminants. On the fuel side, related to biogas conversion to heat and power, anode contamination occurs primarily due to hydrogen sulphide (H2S), halogenated hydrocarbons and siloxanes. On the oxidant side, in the case of retrofit of combustion-based power plants and CO2 separation, cathode contamination by sulphur dioxide (SO2) and nitrogen oxide was investigated. An unexpected effect of SO2 at the cathode that leads to contamination of the anode via the electrolyte was discovered. The effect appears quite dependent on fuel utilisation. A model has been developed and preliminary validation tests under uncontaminated conditions are underway. Work to date has led to a preliminary design of an optimised, industrial-scale gas-cleaning system that will ultimately lead to a pilot-scale gas-cleaning unit. MCFC-CONTEX expects to have major impact on biogas exploitation and on CCS. Advances in this area will have both intermediate and long-term solutions to the growing energy challenges related to global climate change.