FuelCell Energy (FCE) is a leader in clean energy technologies, using molten carbonate fuel cells (MCFCs) to generate low-carbon electricity while supporting hydrogen production and carbon capture. Before a fuel cell stack is ready to operate, it must undergo a time-intensive conditioning process. During conditioning, the fuel cell stack is gradually heated to initiate melting of internal materials. This requires carefully controlled heating to maintain a uniform temperature profile and avoid unwanted heat release. The objective of this project is to reduce conditioning time by 20–50% without compromising cell performance or safety. Our team studied how heat is generated and transferred within the stack using both historical and newly collected differential scanning calorimetry (DSC) data. Using these results, we developed a heat-generation model and simulation that predicts temperature changes and helps determine safer, faster heating strategies. Reducing conditioning time lowers fuel consumption, electrical demand for control systems, and labor required to monitor and manage each cell while also improving overall production efficiency. Even a 24-hour reduction in conditioning time can lower costs by almost 7%. Overall, this project supports FCE’s goals of improving production efficiency while making fuel cell technology more affordable and sustainable.