The Molten Carbonate Fuel Cell (MCFC) is a technology that provides clean electricity and requires carbon dioxide to operate due to its carbonate electrolyte environment. This characteristic offers it an advantage as a technique for carbon capture during fuel cell operation and re-use of captured CO2 during electrolysis mode operation in the Molten Carbonate Electrolysis Cell (MCEC). In both cases, the cell’s feeds must be inspected for any impurities since MCFC/MCEC is highly sensitive to sulfur. Since CO2 as a feed for the cell is captured from the flue gases that contain impurities like SOx, NOx, and others, it is necessary to purify it to reach the MCFC’s tolerance limit. The purpose of this study is to simulate a full process for capturing CO2 and purifying it to fulfill impurity constraints of 1 ppm sulfur for use in MCEC. For this purpose, the conventional MEA-based absorption carbon capture method was created with a real flue gas composition input from a coal-fired power station and associated with two distinct desulfurization processes: wet limestone and cryogenic. According to this study, the wet limestone desulfurization process eliminates almost 100 % of the sulfur; however, the standard cryogenic process couldn’t attain a 1 ppm sulfur limit, promoting for studying a newly optimized cryogenic process with yielded 100 % of sulfur removal. As for the MEA-based absorption process, it captures around 95% of the CO2. The economic assessment revealed that the desulfurization process based on the optimized cryogenic process combined with the MEA capture system provides a lower total cost than the one based on the wet limestone. The latter's high expenses contribute to the requirement of an excessive amount of raw material to attain the threshold of 1 ppm sulfur. This overall analysis demonstrates that the cryogenic approach appears to be the best option for this target, whereas the limestone process requires more improvements to reduce its costs.